To investigate if non-B DNA structures can affect splicing, we explore the distribution of different motifs that are associated with Non-B DNA structures. We calculated the number of these motifs that can be found across splice sites (.num files) and then we calculated the positional enrichment of these across splice sites.
library(readr)
library(data.table)
library(ggplot2)
library(plyr)
library(cowplot)
library(Hmisc)
On this report we compile all the data analysis that lead us to get the final figures. For this, we processed several a
read_dist_table <- function(path){
dist_table <- data.table(read_delim(path,
"\t", escape_double = FALSE, col_names = FALSE,
trim_ws = TRUE))
dist_table <- dist_table[, 2:2001]
dist_table <- data.table(as.data.frame(t(dist_table)))
colnames(dist_table) <- c("Position", "Occurrences")
dist_table[,median:=median(Occurrences)]
dist_table[, Enrrichment:=Occurrences/median]
dist_table[, Position:=Position-1]
return(dist_table)
}
plot_density <- function(up_plus, up_minus, down_plus, down_minus){
up_TOTAL <- merge(up_plus, up_minus, by="Position")
up_TOTAL[,Occurrences:=Occurrences.x+Occurrences.y]
up_TOTAL[,median:=median(Occurrences)]
up_TOTAL[, Enrrichment:=Occurrences/median]
up_TOTAL[, Position:=Position-1]
down_TOTAL <- merge(down_plus, down_minus, by="Position")
down_TOTAL[,Occurrences:=Occurrences.x+Occurrences.y]
down_TOTAL[,median:=median(Occurrences)]
down_TOTAL[, Enrrichment:=Occurrences/median]
down_TOTAL[, Position:=Position-1]
up_TOTAL[ ,exon_pos:="Upstream"]
down_TOTAL[ ,exon_pos:="Downstream"]
TOTAL <- rbind(up_TOTAL, down_TOTAL)
TOTAL$exon_pos <- factor(TOTAL$exon_pos, levels=c("Upstream", "Downstream" ))
p <- ggplot(TOTAL)+
geom_line(aes(x=Position,y=Enrrichment)) +
facet_grid( . ~ exon_pos ) +
theme_bw()
show(p)
TOTAL
}
plot_density_binomial <- function(up_plus, up_minus, down_plus, down_minus, observations, sig){
up_TOTAL <- merge(up_plus, up_minus, by="Position")
up_TOTAL[,Occurrences:=Occurrences.x+Occurrences.y]
up_TOTAL[,Occurrences:=Occurrences.x+Occurrences.y]
up_TOTAL <- cbind(up_TOTAL, up_TOTAL[, binconf(Occurrences, observations, alpha=sig) ])
up_TOTAL[,median:=median(PointEst)]
up_TOTAL[, Enrrichment:=PointEst/median]
up_TOTAL[, Enrrichment_l:=Lower/median]
up_TOTAL[, Enrrichment_u:=Upper/median]
up_TOTAL[, Position:=Position-1]
down_TOTAL <- merge(down_plus, down_minus, by="Position")
down_TOTAL[,Occurrences:=Occurrences.x+Occurrences.y]
down_TOTAL <- cbind(down_TOTAL, down_TOTAL[, binconf(Occurrences, observations, alpha=sig) ])
down_TOTAL[,median:=median(PointEst)]
down_TOTAL[, Enrrichment:=PointEst/median]
down_TOTAL[, Enrrichment_l:=Lower/median]
down_TOTAL[, Enrrichment_u:=Upper/median]
down_TOTAL[, Position:=Position-1]
up_TOTAL[ ,exon_pos:="Upstream"]
down_TOTAL[ ,exon_pos:="Downstream"]
TOTAL <- rbind(up_TOTAL, down_TOTAL)
TOTAL$exon_pos <- factor(TOTAL$exon_pos, levels=c("Upstream", "Downstream" ))
p <- ggplot(TOTAL)+
geom_line(aes(x=Position,y=Enrrichment)) +
geom_ribbon(aes(ymin=Enrrichment_l, ymax=Enrrichment_u, x=Position), alpha=0.3 )+
facet_grid( . ~ exon_pos ) +
theme_bw()
show(p)
return(TOTAL)
}
G4.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/G4.exon.up_plus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/G4.exon.up_plus.list.out.num'
G4.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/G4.exon.down_plus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/G4.exon.down_plus.list.out.num'
G4.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/G4.exon.up_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/G4.exon.up_minus.list.out.num'
G4.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/G4.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/G4.exon.down_minus.list.out.num'
G4.up_minus[,Position:=Position*-1]
G4.down_minus[,Position:=Position*-1]
G4.TOTAL <- plot_density(G4.up_plus, G4.up_minus, G4.down_plus, G4.down_minus)
DR.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/DR.exon.up_plus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/DR.exon.up_plus.list.out.num'
DR.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/DR.exon.down_plus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/DR.exon.down_plus.list.out.num'
DR.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/DR.exon.up_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/DR.exon.up_minus.list.out.num'
DR.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/DR.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/DR.exon.down_minus.list.out.num'
DR.up_minus[,Position:=Position*-1]
DR.down_minus[,Position:=Position*-1]
DR.TOTAL <- plot_density(DR.up_plus, DR.up_minus, DR.down_plus, DR.down_minus)
H_DNA.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/H_DNA.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/H_DNA.exon.down_minus.list.out.num'
H_DNA.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/H_DNA.exon.down_plus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/H_DNA.exon.down_plus.list.out.num'
H_DNA.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/H_DNA.exon.up_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/H_DNA.exon.up_minus.list.out.num'
H_DNA.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/H_DNA.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/H_DNA.exon.down_minus.list.out.num'
H_DNA.up_minus[,Position:=Position*-1]
H_DNA.down_minus[,Position:=Position*-1]
H_DNA.TOTAL <- plot_density(H_DNA.up_plus, H_DNA.up_minus, H_DNA.down_plus, H_DNA.down_minus)
IR.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/IR.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/IR.exon.down_minus.list.out.num'
IR.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/IR.exon.down_plus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/IR.exon.down_plus.list.out.num'
IR.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/IR.exon.up_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/IR.exon.up_minus.list.out.num'
IR.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/IR.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/IR.exon.down_minus.list.out.num'
IR.up_minus[,Position:=Position*-1]
IR.down_minus[,Position:=Position*-1]
IR.TOTAL <- plot_density(IR.up_plus, IR.up_minus, IR.down_plus, IR.down_minus)
MR.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/MR.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/MR.exon.down_minus.list.out.num'
MR.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/MR.exon.down_plus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/MR.exon.down_plus.list.out.num'
MR.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/MR.exon.up_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/MR.exon.up_minus.list.out.num'
MR.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/MR.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/MR.exon.down_minus.list.out.num'
MR.up_minus[,Position:=Position*-1]
MR.down_minus[,Position:=Position*-1]
MR.TOTAL <- plot_density(MR.up_plus, MR.up_minus, MR.down_plus, MR.down_minus)
STR.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/STR.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/STR.exon.down_minus.list.out.num'
STR.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/STR.exon.down_plus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/STR.exon.down_plus.list.out.num'
STR.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/STR.exon.up_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/STR.exon.up_minus.list.out.num'
STR.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/STR.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/STR.exon.down_minus.list.out.num'
STR.up_minus[,Position:=Position*-1]
STR.down_minus[,Position:=Position*-1]
STR.TOTAL <- plot_density(STR.up_plus, STR.up_minus, STR.down_plus, STR.down_minus)
Z_DNA.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/Z_DNA.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/Z_DNA.exon.down_minus.list.out.num'
Z_DNA.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/Z_DNA.exon.down_plus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/Z_DNA.exon.down_plus.list.out.num'
Z_DNA.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/Z_DNA.exon.up_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/Z_DNA.exon.up_minus.list.out.num'
Z_DNA.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/Z_DNA.exon.down_minus.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/Z_DNA.exon.down_minus.list.out.num'
Z_DNA.up_minus[,Position:=Position*-1]
Z_DNA.down_minus[,Position:=Position*-1]
Z_DNA.TOTAL <- plot_density(Z_DNA.up_plus, Z_DNA.up_minus, Z_DNA.down_plus, Z_DNA.down_minus)
G4.TOTAL[, Non_B:="G4"]
DR.TOTAL[, Non_B:="DR"]
H_DNA.TOTAL[, Non_B:="H DNA"]
IR.TOTAL[, Non_B:="IR"]
MR.TOTAL[, Non_B:="MR"]
STR.TOTAL[, Non_B:="STR"]
Z_DNA.TOTAL[, Non_B:="Z DNA"]
Non_B.TOTAL <- rbind(G4.TOTAL, DR.TOTAL, H_DNA.TOTAL, IR.TOTAL, MR.TOTAL, STR.TOTAL, Z_DNA.TOTAL)
Fig1.A <- ggplot(Non_B.TOTAL)+
geom_line(aes(x=Position,y=Enrrichment)) +
xlim(c(-300,300)) +
facet_grid( Non_B ~ exon_pos ) +
theme_bw()
Fig1.A
Non_B.TOTAL.Enrrichment_Peak <- Non_B.TOTAL[ , .(Enrrichment_Peak=max(Enrrichment)) , by = c("Non_B", "exon_pos" )]
write.table(Non_B.TOTAL.Enrrichment_Peak, file = "Non_B.TOTAL.Enrrichment_Peak.txt", append = FALSE, quote = FALSE, sep = "\t",
eol = "\n", na = "NA", dec = ".", row.names = FALSE,
col.names = TRUE, qmethod = c("escape", "double"),
fileEncoding = "")
We calculated the distribution of non-B DNA motifs across quartiles of splice strength, where Q1 are the weakest splice sites and Q4 are the strongest.
Merge_Qs <- function(Qs.list, window_len, strand ) {
Total_Qs <- data.table(rbindlist(Qs.list))
Q_names <- seq(nrow(Total_Qs)/window_len)
Total_Qs[, Q:=rep(Q_names, each=window_len)]
if(strand=="-"){
Total_Qs[,Position:=Position*-1]
}
Total_Qs
}
merge_plus_minus <- function(plus, minus){
TOTAL <- merge(plus, minus, by=c("Position", "Q") )
TOTAL[,Occurrences:=Occurrences.x+Occurrences.y]
TOTAL[,median:=median(Occurrences), by=c("Q")]
TOTAL[, Enrrichment:=Occurrences/median]
TOTAL[, Position:=Position-1]
}
Merge_up_down <- function(Qs.up, Qs.down){
Qs.total <- rbind(Qs.up, Qs.down)
half_n <- nrow(Qs.total)/2
Qs.total[, exon_pos:=rep(c("Upstream", "Downstream"), each=half_n) ]
Qs.total$exon_pos <- factor(Qs.total$exon_pos, levels=c("Upstream", "Downstream" ))
Qs.total$Q <- factor(Qs.total$Q)
Qs.total
}
get_total_Qs <- function(Qs.plus.up.list, Qs.minus.list, Qs.plus.down.list, Qs.minus.down.list, window_len){
Qs.plus.up <- Merge_Qs(Qs.plus.up.list, window_len, strand="+")
Qs.minus.up <- Merge_Qs(Qs.minus.list, window_len, strand="-")
Qs.up <- merge_plus_minus(Qs.plus.up, Qs.minus.up)
Qs.plus.down <- Merge_Qs(Qs.plus.down.list, window_len, strand="+")
Qs.minus.down<- Merge_Qs(Qs.minus.down.list, window_len, strand="-")
Qs.down <- merge_plus_minus(Qs.plus.down, Qs.minus.down)
Qs.total <- Merge_up_down(Qs.up, Qs.down)
Qs.total
}
hg19.nexons <- 123433 + 123936
G4.Q1_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.G4.list.out.num'
G4.Q2_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.G4.list.out.num'
G4.Q3_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.G4.list.out.num'
G4.Q4_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.G4.list.out.num'
G4.Q1_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.G4.list.out.num'
G4.Q2_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.G4.list.out.num'
G4.Q3_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.G4.list.out.num'
G4.Q4_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.G4.list.out.num'
G4.Q1_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.G4.list.out.num'
G4.Q2_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.G4.list.out.num'
G4.Q3_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.G4.list.out.num'
G4.Q4_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.G4.list.out.num'
G4.Q1_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.G4.list.out.num'
G4.Q2_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.G4.list.out.num'
G4.Q3_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.G4.list.out.num'
G4.Q4_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.G4.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.G4.list.out.num'
G4.Qs.plus.up.list <- list(G4.Q1_up_plus, G4.Q2_up_plus, G4.Q3_up_plus, G4.Q4_up_plus)
G4.Qs.minus.list <- list(G4.Q1_up_minus, G4.Q2_up_minus, G4.Q3_up_minus, G4.Q4_up_minus)
G4.Qs.plus.down.list <- list(G4.Q1_down_plus, G4.Q2_down_plus, G4.Q3_down_plus, G4.Q4_down_plus)
G4.Qs.minus.down.list <- list(G4.Q1_down_minus, G4.Q2_down_minus, G4.Q3_down_minus, G4.Q4_down_minus)
G4.window_len = 2000
G4.Qs.total <- get_total_Qs(G4.Qs.plus.up.list, G4.Qs.minus.list, G4.Qs.plus.down.list, G4.Qs.minus.down.list, G4.window_len)
G4.Qs.total$Q <- mapvalues(G4.Qs.total$Q, from =c(1:4), to =c("Q1", "Q2", "Q3", "Q4"))
ggplot(G4.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-150,150)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw()+labs(colour = "Splice site stregth quartile") +
theme(legend.position = "top", legend.direction = "horizontal")
G4.Qs.total.binomial <- cbind(G4.Qs.total, G4.Qs.total[, binconf(Occurrences, hg19.nexons/4) ])
G4.Qs.total.binomial[ , median:=median(PointEst), by=c("exon_pos", "Q")]
G4.Qs.total.binomial[, `:=`(Enrrichment=PointEst/median, Enrrichment_l=Lower/median, Enrrichment_u=Upper/median)]
ggplot(G4.Qs.total.binomial)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
geom_ribbon(aes(x=Position,y=Enrrichment, fill=Q, ymin=Enrrichment_l, ymax=Enrrichment_u), alpha=0.3) +
xlim(c(-150,150)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw()+labs(colour = "Splice site stregth quartile") +
theme(legend.position = "top", legend.direction = "horizontal")
Ignoring unknown aesthetics: y
DR.Q1_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.DRs.list.out.num'
DR.Q2_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.DRs.list.out.num'
DR.Q3_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.DRs.list.out.num'
DR.Q4_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.DRs.list.out.num'
DR.Q1_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.DRs.list.out.num'
DR.Q2_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.DRs.list.out.num'
DR.Q3_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.DRs.list.out.num'
DR.Q4_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.DRs.list.out.num'
DR.Q1_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.DRs.list.out.num'
DR.Q2_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.DRs.list.out.num'
DR.Q3_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.DRs.list.out.num'
DR.Q4_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.DRs.list.out.num'
DR.Q1_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.DRs.list.out.num'
DR.Q2_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.DRs.list.out.num'
DR.Q3_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.DRs.list.out.num'
DR.Q4_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.DRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.DRs.list.out.num'
DR.Qs.plus.up.list <- list(DR.Q1_up_plus, DR.Q2_up_plus, DR.Q3_up_plus, DR.Q4_up_plus)
DR.Qs.minus.list <- list(DR.Q1_up_minus, DR.Q2_up_minus, DR.Q3_up_minus, DR.Q4_up_minus)
DR.Qs.plus.down.list <- list(DR.Q1_down_plus, DR.Q2_down_plus, DR.Q3_down_plus, DR.Q4_down_plus)
DR.Qs.minus.down.list <- list(DR.Q1_down_minus, DR.Q2_down_minus, DR.Q3_down_minus, DR.Q4_down_minus)
DR.window_len = 2000
DR.Qs.total <- get_total_Qs(DR.Qs.plus.up.list, DR.Qs.minus.list, DR.Qs.plus.down.list, DR.Qs.minus.down.list, DR.window_len)
ggplot(DR.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-200,200)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15))+
theme_bw()
NA
NA
NA
H_DNA.Q1_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.H_DNA.list.out.num'
H_DNA.Q2_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.H_DNA.list.out.num'
H_DNA.Q3_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.H_DNA.list.out.num'
H_DNA.Q4_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.H_DNA.list.out.num'
H_DNA.Q1_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.H_DNA.list.out.num'
H_DNA.Q2_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.H_DNA.list.out.num'
H_DNA.Q3_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.H_DNA.list.out.num'
H_DNA.Q4_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.H_DNA.list.out.num'
H_DNA.Q1_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.H_DNA.list.out.num'
H_DNA.Q2_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.H_DNA.list.out.num'
H_DNA.Q3_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.H_DNA.list.out.num'
H_DNA.Q4_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.H_DNA.list.out.num'
H_DNA.Q1_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.H_DNA.list.out.num'
H_DNA.Q2_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.H_DNA.list.out.num'
H_DNA.Q3_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.H_DNA.list.out.num'
H_DNA.Q4_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.H_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.H_DNA.list.out.num'
H_DNA.Qs.plus.up.list <- list(H_DNA.Q1_up_plus, H_DNA.Q2_up_plus, H_DNA.Q3_up_plus, H_DNA.Q4_up_plus)
H_DNA.Qs.minus.list <- list(H_DNA.Q1_up_minus, H_DNA.Q2_up_minus, H_DNA.Q3_up_minus, H_DNA.Q4_up_minus)
H_DNA.Qs.plus.down.list <- list(H_DNA.Q1_down_plus, H_DNA.Q2_down_plus, H_DNA.Q3_down_plus, H_DNA.Q4_down_plus)
H_DNA.Qs.minus.down.list <- list(H_DNA.Q1_down_minus, H_DNA.Q2_down_minus, H_DNA.Q3_down_minus, H_DNA.Q4_down_minus)
H_DNA.window_len = 2000
H_DNA.Qs.total <- get_total_Qs(H_DNA.Qs.plus.up.list, H_DNA.Qs.minus.list, H_DNA.Qs.plus.down.list, H_DNA.Qs.minus.down.list, H_DNA.window_len)
ggplot(H_DNA.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-200,200)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw()
IR.Q1_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.IRs.list.out.num'
IR.Q2_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.IRs.list.out.num'
IR.Q3_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.IRs.list.out.num'
IR.Q4_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.IRs.list.out.num'
IR.Q1_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.IRs.list.out.num'
IR.Q2_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.IRs.list.out.num'
IR.Q3_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.IRs.list.out.num'
IR.Q4_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.IRs.list.out.num'
IR.Q1_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.IRs.list.out.num'
IR.Q2_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.IRs.list.out.num'
IR.Q3_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.IRs.list.out.num'
IR.Q4_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.IRs.list.out.num'
IR.Q1_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.IRs.list.out.num'
IR.Q2_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.IRs.list.out.num'
IR.Q3_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.IRs.list.out.num'
IR.Q4_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.IRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.IRs.list.out.num'
IR.Qs.plus.up.list <- list(IR.Q1_up_plus, IR.Q2_up_plus, IR.Q3_up_plus, IR.Q4_up_plus)
IR.Qs.minus.list <- list(IR.Q1_up_minus, IR.Q2_up_minus, IR.Q3_up_minus, IR.Q4_up_minus)
IR.Qs.plus.down.list <- list(IR.Q1_down_plus, IR.Q2_down_plus, IR.Q3_down_plus, IR.Q4_down_plus)
IR.Qs.minus.down.list <- list(IR.Q1_down_minus, IR.Q2_down_minus, IR.Q3_down_minus, IR.Q4_down_minus)
IR.window_len = 2000
IR.Qs.total <- get_total_Qs(IR.Qs.plus.up.list, IR.Qs.minus.list, IR.Qs.plus.down.list, IR.Qs.minus.down.list, IR.window_len)
ggplot(IR.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-200,200)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw()
MR.Q1_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.MRs.list.out.num'
MR.Q2_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.MRs.list.out.num'
MR.Q3_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.MRs.list.out.num'
MR.Q4_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.MRs.list.out.num'
MR.Q1_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.MRs.list.out.num'
MR.Q2_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.MRs.list.out.num'
MR.Q3_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.MRs.list.out.num'
MR.Q4_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.MRs.list.out.num'
MR.Q1_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.MRs.list.out.num'
MR.Q2_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.MRs.list.out.num'
MR.Q3_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.MRs.list.out.num'
MR.Q4_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.MRs.list.out.num'
MR.Q1_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.MRs.list.out.num'
MR.Q2_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.MRs.list.out.num'
MR.Q3_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.MRs.list.out.num'
MR.Q4_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.MRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.MRs.list.out.num'
MR.Qs.plus.up.list <- list(MR.Q1_up_plus, MR.Q2_up_plus, MR.Q3_up_plus, MR.Q4_up_plus)
MR.Qs.minus.list <- list(MR.Q1_up_minus, MR.Q2_up_minus, MR.Q3_up_minus, MR.Q4_up_minus)
MR.Qs.plus.down.list <- list(MR.Q1_down_plus, MR.Q2_down_plus, MR.Q3_down_plus, MR.Q4_down_plus)
MR.Qs.minus.down.list <- list(MR.Q1_down_minus, MR.Q2_down_minus, MR.Q3_down_minus, MR.Q4_down_minus)
MR.window_len = 2000
MR.Qs.total <- get_total_Qs(MR.Qs.plus.up.list, MR.Qs.minus.list, MR.Qs.plus.down.list, MR.Qs.minus.down.list, window_len)
ggplot(MR.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-200,200)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw()
STR.Q1_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.STRs.list.out.num'
STR.Q2_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.STRs.list.out.num'
STR.Q3_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.STRs.list.out.num'
STR.Q4_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.STRs.list.out.num'
STR.Q1_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.STRs.list.out.num'
STR.Q2_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.STRs.list.out.num'
STR.Q3_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.STRs.list.out.num'
STR.Q4_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.STRs.list.out.num'
STR.Q1_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.STRs.list.out.num'
STR.Q2_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.STRs.list.out.num'
STR.Q3_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.STRs.list.out.num'
STR.Q4_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.STRs.list.out.num'
STR.Q1_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.STRs.list.out.num'
STR.Q2_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.STRs.list.out.num'
STR.Q3_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.STRs.list.out.num'
STR.Q4_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.STRs.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.STRs.list.out.num'
STR.Qs.plus.up.list <- list(STR.Q1_up_plus, STR.Q2_up_plus, STR.Q3_up_plus, STR.Q4_up_plus)
STR.Qs.minus.list <- list(STR.Q1_up_minus, STR.Q2_up_minus, STR.Q3_up_minus, STR.Q4_up_minus)
STR.Qs.plus.down.list <- list(STR.Q1_down_plus, STR.Q2_down_plus, STR.Q3_down_plus, STR.Q4_down_plus)
STR.Qs.minus.down.list <- list(STR.Q1_down_minus, STR.Q2_down_minus, STR.Q3_down_minus, STR.Q4_down_minus)
STR.window_len = 2000
STR.Qs.total <- get_total_Qs(STR.Qs.plus.up.list, STR.Qs.minus.list, STR.Qs.plus.down.list, STR.Qs.minus.down.list, STR.window_len)
ggplot(STR.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-200,200)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw()
Z_DNA.Q1_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q1.bed.Z_DNA.list.out.num'
Z_DNA.Q2_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q2.bed.Z_DNA.list.out.num'
Z_DNA.Q3_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q3.bed.Z_DNA.list.out.num'
Z_DNA.Q4_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_plus.q4.bed.Z_DNA.list.out.num'
Z_DNA.Q1_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q1.bed.Z_DNA.list.out.num'
Z_DNA.Q2_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q2.bed.Z_DNA.list.out.num'
Z_DNA.Q3_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q3.bed.Z_DNA.list.out.num'
Z_DNA.Q4_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_plus.q4.bed.Z_DNA.list.out.num'
Z_DNA.Q1_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q1.bed.Z_DNA.list.out.num'
Z_DNA.Q2_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q2.bed.Z_DNA.list.out.num'
Z_DNA.Q3_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q3.bed.Z_DNA.list.out.num'
Z_DNA.Q4_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.up_minus.q4.bed.Z_DNA.list.out.num'
Z_DNA.Q1_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q1.bed.Z_DNA.list.out.num'
Z_DNA.Q2_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q2.bed.Z_DNA.list.out.num'
Z_DNA.Q3_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q3.bed.Z_DNA.list.out.num'
Z_DNA.Q4_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.Z_DNA.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/All_non_Bs/q1_q4/exon.down_minus.q4.bed.Z_DNA.list.out.num'
Z_DNA.Qs.plus.up.list <- list(Z_DNA.Q1_up_plus, Z_DNA.Q2_up_plus, Z_DNA.Q3_up_plus, Z_DNA.Q4_up_plus)
Z_DNA.Qs.minus.list <- list(Z_DNA.Q1_up_minus, Z_DNA.Q2_up_minus, Z_DNA.Q3_up_minus, Z_DNA.Q4_up_minus)
Z_DNA.Qs.plus.down.list <- list(Z_DNA.Q1_down_plus, Z_DNA.Q2_down_plus, Z_DNA.Q3_down_plus, Z_DNA.Q4_down_plus)
Z_DNA.Qs.minus.down.list <- list(Z_DNA.Q1_down_minus, Z_DNA.Q2_down_minus, Z_DNA.Q3_down_minus, Z_DNA.Q4_down_minus)
Z_DNA.window_len = 2000
Z_DNA.Qs.total <- get_total_Qs(Z_DNA.Qs.plus.up.list, Z_DNA.Qs.minus.list, Z_DNA.Qs.plus.down.list, Z_DNA.Qs.minus.down.list, Z_DNA.window_len)
ggplot(Z_DNA.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-200,200)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw()
G4.Qs.total[, Non_B:="G4"]
DR.Qs.total[, Non_B:="DR"]
H_DNA.Qs.total[, Non_B:="H-DNA"]
IR.Qs.total[, Non_B:="IR"]
MR.Qs.total[, Non_B:="MR"]
STR.Qs.total[, Non_B:="STR"]
Z_DNA.Qs.total[, Non_B:="Z-DNA"]
Non_B.Qs.TOTAL <- rbind(G4.Qs.total, DR.Qs.total, H_DNA.Qs.total, IR.Qs.total, MR.Qs.total, STR.Qs.total, Z_DNA.Qs.total)
Non_B.Qs.TOTAL$Q <- mapvalues(Non_B.Qs.TOTAL$Q, from =c(1:4), to =c("Q1", "Q2", "Q3", "Q4"))
ggplot(Non_B.Qs.TOTAL)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-150,150)) +
facet_grid( Non_B ~ exon_pos ) +
labs(colour = "Splice site stregth quartile") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
Non_B.Qs.TOTAL.Enrrichment_Peak <- Non_B.Qs.TOTAL[ , .(Enrrichment_Peak=max(Enrrichment)) , by= c("Non_B", "exon_pos", "Q")]
write.table(Non_B.Qs.TOTAL.Enrrichment_Peak, file = "Non_B.Qs.TOTAL.Enrrichment_Peak.txt", append = FALSE, quote = FALSE, sep = "\t",
eol = "\n", na = "NA", dec = ".", row.names = FALSE,
col.names = TRUE, qmethod = c("escape", "double"),
fileEncoding = "")
To investigate if the distribution of non-B DNA motifs is biased by transcription direction, we generate .num files where the counts were separated by template and non templated strands:
G4.template.Q1_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q1.bed.G4s_minus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q1.bed.G4s_minus_plus.list.final.num'
G4.template.Q2_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q2.bed.G4s_minus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q2.bed.G4s_minus_plus.list.final.num'
G4.template.Q3_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q3.bed.G4s_minus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q3.bed.G4s_minus_plus.list.final.num'
G4.template.Q4_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q4.bed.G4s_minus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q4.bed.G4s_minus_plus.list.final.num'
G4.template.Q1_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q1.bed.G4s_plus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q1.bed.G4s_plus_minus.list.final.num'
G4.template.Q2_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q2.bed.G4s_plus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q2.bed.G4s_plus_minus.list.final.num'
G4.template.Q3_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q3.bed.G4s_plus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q3.bed.G4s_plus_minus.list.final.num'
G4.template.Q4_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q4.bed.G4s_plus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q4.bed.G4s_plus_minus.list.final.num'
G4.template.Q1_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q1.bed.G4s_minus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q1.bed.G4s_minus_plus.list.final.num'
G4.template.Q2_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q2.bed.G4s_minus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q2.bed.G4s_minus_plus.list.final.num'
G4.template.Q3_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q3.bed.G4s_minus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q3.bed.G4s_minus_plus.list.final.num'
G4.template.Q4_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q4.bed.G4s_minus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q4.bed.G4s_minus_plus.list.final.num'
G4.template.Q1_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q1.bed.G4s_plus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q1.bed.G4s_plus_minus.list.final.num'
G4.template.Q2_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q2.bed.G4s_plus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q2.bed.G4s_plus_minus.list.final.num'
G4.template.Q3_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q3.bed.G4s_plus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q3.bed.G4s_plus_minus.list.final.num'
G4.template.Q4_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q4.bed.G4s_plus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q4.bed.G4s_plus_minus.list.final.num'
G4.non_template.Q1_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q1.bed.G4s_plus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q1.bed.G4s_plus_plus.list.final.num'
G4.non_template.Q2_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q2.bed.G4s_plus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q2.bed.G4s_plus_plus.list.final.num'
G4.non_template.Q3_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q3.bed.G4s_plus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q3.bed.G4s_plus_plus.list.final.num'
G4.non_template.Q4_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q4.bed.G4s_plus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_plus.q4.bed.G4s_plus_plus.list.final.num'
G4.non_template.Q1_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q1.bed.G4s_minus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q1.bed.G4s_minus_minus.list.final.num'
G4.non_template.Q2_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q2.bed.G4s_minus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q2.bed.G4s_minus_minus.list.final.num'
G4.non_template.Q3_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q3.bed.G4s_minus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q3.bed.G4s_minus_minus.list.final.num'
G4.non_template.Q4_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q4.bed.G4s_minus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.up_minus.q4.bed.G4s_minus_minus.list.final.num'
G4.non_template.Q1_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q1.bed.G4s_plus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q1.bed.G4s_plus_plus.list.final.num'
G4.non_template.Q2_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q2.bed.G4s_plus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q2.bed.G4s_plus_plus.list.final.num'
G4.non_template.Q3_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q3.bed.G4s_plus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q3.bed.G4s_plus_plus.list.final.num'
G4.non_template.Q4_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q4.bed.G4s_plus_plus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_plus.q4.bed.G4s_plus_plus.list.final.num'
G4.non_template.Q1_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q1.bed.G4s_minus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q1.bed.G4s_minus_minus.list.final.num'
G4.non_template.Q2_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q2.bed.G4s_minus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q2.bed.G4s_minus_minus.list.final.num'
G4.non_template.Q3_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q3.bed.G4s_minus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q3.bed.G4s_minus_minus.list.final.num'
G4.non_template.Q4_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q4.bed.G4s_minus_minus.list.final.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/template_non_template/exon.down_minus.q4.bed.G4s_minus_minus.list.final.num'
G4.template.Qs.plus.up.list <- list(G4.template.Q1_up_plus, G4.template.Q2_up_plus, G4.template.Q3_up_plus, G4.template.Q4_up_plus)
G4.template.Qs.minus.list <- list(G4.template.Q1_up_minus, G4.template.Q2_up_minus, G4.template.Q3_up_minus, G4.template.Q4_up_minus)
G4.template.Qs.plus.down.list <- list(G4.template.Q1_down_plus, G4.template.Q2_down_plus, G4.template.Q3_down_plus, G4.template.Q4_down_plus)
G4.template.Qs.minus.down.list <- list(G4.template.Q1_down_minus, G4.template.Q2_down_minus, G4.template.Q3_down_minus, G4.template.Q4_down_minus)
G4.template.window_len = 2000
G4.template.Qs.total <- get_total_Qs(G4.template.Qs.plus.up.list, G4.template.Qs.minus.list, G4.template.Qs.plus.down.list, G4.template.Qs.minus.down.list, window_len)
G4.non_template.Qs.plus.up.list <- list(G4.non_template.Q1_up_plus, G4.non_template.Q2_up_plus, G4.non_template.Q3_up_plus, G4.non_template.Q4_up_plus)
G4.non_template.Qs.minus.list <- list(G4.non_template.Q1_up_minus, G4.non_template.Q2_up_minus, G4.non_template.Q3_up_minus, G4.non_template.Q4_up_minus)
G4.non_template.Qs.plus.down.list <- list(G4.non_template.Q1_down_plus, G4.non_template.Q2_down_plus, G4.non_template.Q3_down_plus, G4.non_template.Q4_down_plus)
G4.non_template.Qs.minus.down.list <- list(G4.non_template.Q1_down_minus, G4.non_template.Q2_down_minus, G4.non_template.Q3_down_minus, G4.non_template.Q4_down_minus)
G4.non_template.window_len = 2000
G4.non_template.Qs.total <- get_total_Qs(G4.non_template.Qs.plus.up.list, G4.non_template.Qs.minus.list, G4.non_template.Qs.plus.down.list, G4.non_template.Qs.minus.down.list, window_len)
G4.template.Qs.total
Position Q Occurrences.x median.x Enrrichment.x Occurrences.y median.y Enrrichment.y Occurrences median Enrrichment exon_pos
1: -1000 1 147 179 0.8212291 152 175 0.8685714 299 351 0.8518519 Upstream
2: -1000 2 126 134 0.9402985 141 135 1.0444444 267 268 0.9962687 Upstream
3: -1000 3 100 99 1.0101010 94 94 1.0000000 194 192 1.0104167 Upstream
4: -1000 4 63 66 0.9545455 74 65 1.1384615 137 131 1.0458015 Upstream
5: -999 1 149 179 0.8324022 150 175 0.8571429 299 351 0.8518519 Upstream
---
15988: 997 4 99 108 0.9166667 104 104 1.0000000 203 211 0.9620853 Downstream
15989: 998 1 119 137 0.8686131 111 129 0.8604651 230 266 0.8646617 Downstream
15990: 998 2 109 128 0.8515625 117 127 0.9212598 226 252 0.8968254 Downstream
15991: 998 3 106 110 0.9636364 109 109 1.0000000 215 217 0.9907834 Downstream
15992: 998 4 96 108 0.8888889 104 104 1.0000000 200 211 0.9478673 Downstream
G4.non_template.Qs.total
Position Q Occurrences.x median.x Enrrichment.x Occurrences.y median.y Enrrichment.y Occurrences median Enrrichment exon_pos
1: -1000 1 193 202 0.9554455 174 200 0.8700000 367 406 0.9039409 Upstream
2: -1000 2 148 161 0.9192547 120 149 0.8053691 268 309 0.8673139 Upstream
3: -1000 3 124 122 1.0163934 113 108 1.0462963 237 229 1.0349345 Upstream
4: -1000 4 84 74 1.1351351 70 70 1.0000000 154 144 1.0694444 Upstream
5: -999 1 193 202 0.9554455 177 200 0.8850000 370 406 0.9113300 Upstream
---
15988: 997 4 102 114 0.8947368 99 109 0.9082569 201 225 0.8933333 Downstream
15989: 998 1 123 154 0.7987013 128 136 0.9411765 251 289 0.8685121 Downstream
15990: 998 2 128 147 0.8707483 114 139 0.8201439 242 288 0.8402778 Downstream
15991: 998 3 108 125 0.8640000 90 122 0.7377049 198 249 0.7951807 Downstream
15992: 998 4 98 114 0.8596491 99 109 0.9082569 197 225 0.8755556 Downstream
G4.template_non_template.Qs.total <- rbind(G4.template.Qs.total, G4.non_template.Qs.total)
half_n <- nrow(G4.template_non_template.Qs.total)/2
G4.template_non_template.Qs.total[, Strand:=rep(c("Template", "Non-template"), each=half_n) ]
G4.template_non_template.Qs.total$Strand <- factor(G4.template_non_template.Qs.total$Strand, levels=c("Template", "Non-template" ))
G4.template_non_template.Qs.total$Q <- mapvalues(G4.template_non_template.Qs.total$Q, from =c(1:4), to =c("Q1", "Q2", "Q3", "Q4"))
G4.template_non_template.Qs.total.binomial <- cbind(G4.template_non_template.Qs.total, G4.template_non_template.Qs.total[, binconf(Occurrences, hg19.nexons/8) ])
G4.template_non_template.Qs.total.binomial[, median:=NULL]
G4.template_non_template.Qs.total.binomial[ , median:=median(PointEst), by=c("exon_pos", "Q", "Strand")]
G4.template_non_template.Qs.total.binomial[, `:=`(Enrrichment=PointEst/median, Enrrichment_l=Lower/median, Enrrichment_u=Upper/median)]
Fig2.A <- ggplot(G4.template_non_template.Qs.total.binomial)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
geom_ribbon(aes(x=Position, fill=Q, ymin=Enrrichment_l, ymax=Enrrichment_u), alpha=0.3) +
xlim(c(-150,150)) +
facet_grid( Strand ~ exon_pos ) +
labs(colour = "Splice site stregth quartile") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
Fig2.A
G4.template_non_template.total <- G4.template_non_template.Qs.total[ , .(Occurrences=sum(Occurrences)) , by=c("Strand", "exon_pos", "Position")]
G4.template_non_template.total[ , median:=median(Occurrences) , by=c("Strand", "exon_pos")]
G4.template_non_template.total[ , Enrrichment:=Occurrences/median , by=c("Strand", "exon_pos", "Position")]
ggplot(G4.template_non_template.total)+
geom_line(aes(x=Position,y=Enrrichment)) +
xlim(c(-150,150)) +
facet_grid( Strand ~ exon_pos ) +
labs(colour = "Splice site stregth quartile") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
G4.template_non_template.total_Peak <- G4.template_non_template.total[ , .(Enrrichment_Peak=max(Enrrichment)) , by= c("Strand", "exon_pos")]
write.table(G4.template_non_template.total_Peak, file = "G4.template_non_template.total_Peak.txt", append = FALSE, quote = FALSE, sep = "\t",
eol = "\n", na = "NA", dec = ".", row.names = FALSE,
col.names = TRUE, qmethod = c("escape", "double"),
fileEncoding = "")
G4.template_non_template.Qs.total.Enrrichment_Peak <- G4.template_non_template.Qs.total[ , .(Enrrichment_Peak=max(Enrrichment)) , by= c( "exon_pos", "Q", "Strand" )]
write.table(G4.template_non_template.Qs.total.Enrrichment_Peak, file = "G4.template_non_template.Qs.total.Enrrichment_Peak.txt", append = FALSE, quote = FALSE, sep = "\t",
eol = "\n", na = "NA", dec = ".", row.names = FALSE,
col.names = TRUE, qmethod = c("escape", "double"),
fileEncoding = "")
Here we explored the enrichment of G-quadruplexes with different G-run length
G1_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_plus.bed.Single_G_runs.list.out.num")
G2_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_plus.bed.Twice_G_runs.list.out.num")
G3_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_plus.bed.Three_G_runs.list.out.num")
G4_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_plus.bed.Four_G_runs.list.out.num")
G5_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_plus.bed.Five_G_runs.list.out.num")
G6_up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_plus.bed.Six_G_runs.list.out.num")
G1_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_minus.bed.Single_G_runs.list.out.num")
G2_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_minus.bed.Twice_G_runs.list.out.num")
G3_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_minus.bed.Three_G_runs.list.out.num")
G4_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_minus.bed.Four_G_runs.list.out.num")
G5_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_minus.bed.Five_G_runs.list.out.num")
G6_up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.up_minus.bed.Six_G_runs.list.out.num")
G1_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_plus.bed.Single_G_runs.list.out.num")
G2_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_plus.bed.Twice_G_runs.list.out.num")
G3_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_plus.bed.Three_G_runs.list.out.num")
G4_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_plus.bed.Four_G_runs.list.out.num")
G5_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_plus.bed.Five_G_runs.list.out.num")
G6_down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_plus.bed.Six_G_runs.list.out.num")
G1_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_minus.bed.Single_G_runs.list.out.num")
G2_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_minus.bed.Twice_G_runs.list.out.num")
G3_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_minus.bed.Three_G_runs.list.out.num")
G4_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_minus.bed.Four_G_runs.list.out.num") #missing
G5_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_minus.bed.Five_G_runs.list.out.num")
G6_down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/G4_runs/exon.down_minus.bed.Six_G_runs.list.out.num")
Gruns.up_plus.list <- list(G1_up_plus, G2_up_plus, G3_up_plus, G4_up_plus, G5_up_plus, G6_up_plus)
Gruns.up_minus.list <- list(G1_up_minus, G2_up_minus, G3_up_minus, G4_up_minus, G5_up_minus, G6_up_minus)
Gruns.down_plus.list <- list(G1_down_plus, G2_down_plus, G3_down_plus, G4_down_plus, G5_down_plus, G6_down_plus)
Gruns.down_minus.list <- list(G1_down_minus, G2_down_minus, G3_down_minus, G4_down_minus, G5_down_minus, G6_down_minus)
Gruns.window_len = 2000
Gruns.total <- get_total_Qs(Gruns.up_plus.list, Gruns.up_minus.list, Gruns.down_plus.list, Gruns.down_minus.list, Gruns.window_len)
Gruns.total[, G_run_length:=Q]
Fig2.B
Error in FUN(X[[i]], ...) : object 'Enrrichment_l' not found
Gruns.total.Enrrichment_Peak <- Gruns.total[ , .(Enrrichment_Peak=max(Enrrichment)) , by= c( "exon_pos", "G_run_length")]
write.table(Gruns.total.Enrrichment_Peak, file = "Gruns.total.Enrrichment_Peak.txt", append = FALSE, quote = FALSE, sep = "\t",
eol = "\n", na = "NA", dec = ".", row.names = FALSE,
col.names = TRUE, qmethod = c("escape", "double"),
fileEncoding = "")
We analyzed the G4 enrichment across splice sites from different species
susScr11.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/susScr11.exon.up_plus.bed.score.susScr11.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/susScr11.exon.up_plus.bed.score.susScr11.txt..list.out.num'
susScr11.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/susScr11.exon.down_plus.bed.score.susScr11.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/susScr11.exon.down_plus.bed.score.susScr11.txt..list.out.num'
susScr11.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/susScr11.exon.up_minus.bed.score.susScr11.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/susScr11.exon.up_minus.bed.score.susScr11.txt..list.out.num'
susScr11.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/susScr11.exon.down_minus.bed.score.susScr11.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/susScr11.exon.down_minus.bed.score.susScr11.txt..list.out.num'
susScr11.up_minus[,Position:=Position*-1]
susScr11.down_minus[,Position:=Position*-1]
susScr11.TOTAL <- plot_density(susScr11.up_plus, susScr11.up_minus, susScr11.down_plus, susScr11.down_minus)
TAIR10.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/TAIR10.exon.up_plus.bed.score.TAIR10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/TAIR10.exon.up_plus.bed.score.TAIR10.txt..list.out.num'
TAIR10.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/TAIR10.exon.down_plus.bed.score.TAIR10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/TAIR10.exon.down_plus.bed.score.TAIR10.txt..list.out.num'
TAIR10.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/TAIR10.exon.up_minus.bed.score.TAIR10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/TAIR10.exon.up_minus.bed.score.TAIR10.txt..list.out.num'
TAIR10.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/TAIR10.exon.down_minus.bed.score.TAIR10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/TAIR10.exon.down_minus.bed.score.TAIR10.txt..list.out.num'
TAIR10.up_minus[,Position:=Position*-1]
TAIR10.down_minus[,Position:=Position*-1]
TAIR10.TOTAL <- plot_density(TAIR10.up_plus, TAIR10.up_minus, TAIR10.down_plus, TAIR10.down_minus)
anoCar2.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/anoCar2.exon.up_plus.bed.score.anoCar2.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/anoCar2.exon.up_plus.bed.score.anoCar2.txt..list.out.num'
anoCar2.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/anoCar2.exon.down_plus.bed.score.anoCar2.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/anoCar2.exon.down_plus.bed.score.anoCar2.txt..list.out.num'
anoCar2.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/anoCar2.exon.up_minus.bed.score.anoCar2.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/anoCar2.exon.up_minus.bed.score.anoCar2.txt..list.out.num'
anoCar2.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/anoCar2.exon.down_minus.bed.score.anoCar2.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/anoCar2.exon.down_minus.bed.score.anoCar2.txt..list.out.num'
anoCar2.up_minus[,Position:=Position*-1]
anoCar2.down_minus[,Position:=Position*-1]
anoCar2.TOTAL <- plot_density(anoCar2.up_plus, anoCar2.up_minus, anoCar2.down_plus, anoCar2.down_minus)
xenTro9.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/xenTro9.exon.up_plus.bed.score.xenTro9.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/xenTro9.exon.up_plus.bed.score.xenTro9.txt..list.out.num'
xenTro9.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/xenTro9.exon.down_plus.bed.score.xenTro9.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/xenTro9.exon.down_plus.bed.score.xenTro9.txt..list.out.num'
xenTro9.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/xenTro9.exon.up_minus.bed.score.xenTro9.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/xenTro9.exon.up_minus.bed.score.xenTro9.txt..list.out.num'
xenTro9.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/xenTro9.exon.down_minus.bed.score.xenTro9.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/xenTro9.exon.down_minus.bed.score.xenTro9.txt..list.out.num'
xenTro9.up_minus[,Position:=Position*-1]
xenTro9.down_minus[,Position:=Position*-1]
xenTro9.TOTAL <- plot_density(xenTro9.up_plus, xenTro9.up_minus, xenTro9.down_plus, xenTro9.down_minus)
ce10.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/ce10.exon.up_plus.bed.score.ce10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/ce10.exon.up_plus.bed.score.ce10.txt..list.out.num'
ce10.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/ce10.exon.down_plus.bed.score.ce10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/ce10.exon.down_plus.bed.score.ce10.txt..list.out.num'
ce10.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/ce10.exon.up_minus.bed.score.ce10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/ce10.exon.up_minus.bed.score.ce10.txt..list.out.num'
ce10.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/ce10.exon.down_minus.bed.score.ce10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/ce10.exon.down_minus.bed.score.ce10.txt..list.out.num'
ce10.up_minus[,Position:=Position*-1]
ce10.down_minus[,Position:=Position*-1]
ce10.TOTAL <- plot_density(ce10.up_plus, ce10.up_minus, ce10.down_plus, ce10.down_minus)
danRer11.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/danRer11.exon.up_plus.bed.score.danRer11.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/danRer11.exon.up_plus.bed.score.danRer11.txt..list.out.num'
danRer11.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/danRer11.exon.down_plus.bed.score.danRer11.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/danRer11.exon.down_plus.bed.score.danRer11.txt..list.out.num'
danRer11.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/danRer11.exon.up_minus.bed.score.danRer11.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/danRer11.exon.up_minus.bed.score.danRer11.txt..list.out.num'
danRer11.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/danRer11.exon.down_minus.bed.score.danRer11.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/danRer11.exon.down_minus.bed.score.danRer11.txt..list.out.num'
danRer11.up_minus[,Position:=Position*-1]
danRer11.down_minus[,Position:=Position*-1]
danRer11.TOTAL <- plot_density(danRer11.up_plus, danRer11.up_minus, danRer11.down_plus, danRer11.down_minus)
mm10.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/mm10.exon.up_plus.bed.score.mm10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/mm10.exon.up_plus.bed.score.mm10.txt..list.out.num'
mm10.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/mm10.exon.down_plus.bed.score.mm10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/mm10.exon.down_plus.bed.score.mm10.txt..list.out.num'
mm10.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/mm10.exon.up_minus.bed.score.mm10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/mm10.exon.up_minus.bed.score.mm10.txt..list.out.num'
mm10.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/mm10.exon.down_minus.bed.score.mm10.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/mm10.exon.down_minus.bed.score.mm10.txt..list.out.num'
mm10.up_minus[,Position:=Position*-1]
mm10.down_minus[,Position:=Position*-1]
mm10.TOTAL <- plot_density(mm10.up_plus, mm10.up_minus, mm10.down_plus, mm10.down_minus)
hg19.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/hg19.exon.up_plus.bed.score.hg19.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/hg19.exon.up_plus.bed.score.hg19.txt..list.out.num'
hg19.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/hg19.exon.down_plus.bed.score.hg19.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/hg19.exon.down_plus.bed.score.hg19.txt..list.out.num'
hg19.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/hg19.exon.up_minus.bed.score.hg19.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/hg19.exon.up_minus.bed.score.hg19.txt..list.out.num'
hg19.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/hg19.exon.down_minus.bed.score.hg19.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/hg19.exon.down_minus.bed.score.hg19.txt..list.out.num'
hg19.up_minus[,Position:=Position*-1]
hg19.down_minus[,Position:=Position*-1]
hg19.TOTAL <- plot_density(hg19.up_plus, hg19.up_minus, hg19.down_plus, hg19.down_minus)
dm6.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/dm6.exon.up_plus.bed.score.dm6.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/dm6.exon.up_plus.bed.score.dm6.txt..list.out.num'
dm6.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/dm6.exon.down_plus.bed.score.dm6.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/dm6.exon.down_plus.bed.score.dm6.txt..list.out.num'
dm6.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/dm6.exon.up_minus.bed.score.dm6.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/dm6.exon.up_minus.bed.score.dm6.txt..list.out.num'
dm6.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/dm6.exon.down_minus.bed.score.dm6.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/dm6.exon.down_minus.bed.score.dm6.txt..list.out.num'
dm6.up_minus[,Position:=Position*-1]
dm6.down_minus[,Position:=Position*-1]
dm6.TOTAL <- plot_density(dm6.up_plus, dm6.up_minus, dm6.down_plus, dm6.down_minus)
galGal5.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/galGal5.exon.up_plus.bed.score.galGal5.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/galGal5.exon.up_plus.bed.score.galGal5.txt..list.out.num'
galGal5.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/galGal5.exon.down_plus.bed.score.galGal5.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/galGal5.exon.down_plus.bed.score.galGal5.txt..list.out.num'
galGal5.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/galGal5.exon.up_minus.bed.score.galGal5.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/galGal5.exon.up_minus.bed.score.galGal5.txt..list.out.num'
galGal5.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/galGal5.exon.down_minus.bed.score.galGal5.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/galGal5.exon.down_minus.bed.score.galGal5.txt..list.out.num'
galGal5.up_minus[,Position:=Position*-1]
galGal5.down_minus[,Position:=Position*-1]
galGal5.TOTAL <- plot_density(galGal5.up_plus, galGal5.up_minus, galGal5.down_plus, galGal5.down_minus)
sacCer.up_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/sacCer3.exon.up_plus.bed.score.sacCer3.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/sacCer3.exon.up_plus.bed.score.sacCer3.txt..list.out.num'
sacCer.down_plus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/sacCer3.exon.down_plus.bed.score.sacCer3.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/sacCer3.exon.down_plus.bed.score.sacCer3.txt..list.out.num'
sacCer.up_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/sacCer3.exon.up_minus.bed.score.sacCer3.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/sacCer3.exon.up_minus.bed.score.sacCer3.txt..list.out.num'
sacCer.down_minus <- read_dist_table("~/Google_Drive/Results/Non_B/Evolution/Num/sacCer3.exon.down_minus.bed.score.sacCer3.txt..list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/Evolution/Num/sacCer3.exon.down_minus.bed.score.sacCer3.txt..list.out.num'
sacCer.up_minus[,Position:=Position*-1]
sacCer.down_minus[,Position:=Position*-1]
sacCer.TOTAL <- plot_density(sacCer.up_plus, sacCer.up_minus, sacCer.down_plus, sacCer.down_minus)
galGal5.up_plus[, rep(Position, Occurrences)]
[1] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[32] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[63] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[94] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[125] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[156] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[187] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[218] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[249] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[280] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[311] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[342] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[373] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[404] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[435] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[466] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[497] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[528] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[559] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[590] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[621] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[652] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[683] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
[714] -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999
[745] -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999
[776] -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999
[807] -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999
[838] -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999
[869] -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999
[900] -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999
[931] -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999
[962] -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999
[993] -999 -999 -999 -999 -999 -999 -999 -999
[ reached getOption("max.print") -- omitted 1276779 entries ]
galGal5.up <- merge(galGal5.down_plus, galGal5.down_minus, by="Position")
galGal5.up[, Occurrences:= Occurrences.x + Occurrences.y]
galGal5.up.melt <- galGal5.up[, rep(Position, Occurrences)]
galGal5.up.melt <- data.table(cbind(galGal5.up.melt, "Up"))
colnames(galGal5.up.melt) <- c("dist", "pos")
galGal5.up.melt$dist <- as.numeric(as.character(galGal5.up.melt$dist))
ggplot(galGal5.up.melt) +
geom_line(aes(dist), stat="density")
All.species.TOTAL <- rbind(ce10.TOTAL, dm6.TOTAL, TAIR10.TOTAL )
ggplot(All.species.TOTAL)+
geom_line(aes(x=Position,y=Enrrichment, color=species)) +
xlim(c(-300,300)) +
ggtitle( "Non-vertebrates") +
facet_grid( . ~ exon_pos ) +
theme(plot.title = element_text(hjust = 0.5)) +
theme_bw()
Here we analized the intron size of distribution of exon which are flanked by G4 (on an 100nt window)
intron_size_upstream_non_template <- rbind(fread('/Users/gp7/Google_Drive/Results/Non_B/Intron_size/Introns.hg19_upstream_100nt_window.bed.plus_strand_genome.plus_G4s'),
fread('/Users/gp7/Google_Drive/Results/Non_B/Intron_size/Introns.hg19_upstream_100nt_window.bed.minus_strand_genome.minus_G4s'))
intron_size_downstream_non_template <- rbind(fread('/Users/gp7/Google_Drive/Results/Non_B/Intron_size/Introns.hg19_downstream_100nt_window.bed.plus_strand_genome.plus_G4s'),
fread('/Users/gp7/Google_Drive/Results/Non_B/Intron_size/Introns.hg19_downstream_100nt_window.bed.minus_strand_genome.minus_G4s'))
intron_size_upstream_template <- rbind(fread('/Users/gp7/Google_Drive/Results/Non_B/Intron_size/Introns.hg19_upstream_100nt_window.bed.plus_strand_genome.minus_G4s'),
fread('/Users/gp7/Google_Drive/Results/Non_B/Intron_size/Introns.hg19_upstream_100nt_window.bed.minus_strand_genome.plus_G4s'))
intron_size_downstream_template <- rbind(fread('/Users/gp7/Google_Drive/Results/Non_B/Intron_size/Introns.hg19_downstream_100nt_window.bed.minus_strand_genome.plus_G4s'),
fread('/Users/gp7/Google_Drive/Results/Non_B/Intron_size/Introns.hg19_downstream_100nt_window.bed.plus_strand_genome.minus_G4s'))
intron_size_upstream_non_template[ , `:=`(exon_pos="upstream", strand="non_template") ]
intron_size_downstream_non_template[ , `:=`(exon_pos="downstream", strand="non_template") ]
intron_size_upstream_template[ , `:=`(exon_pos="upstream", strand="template") ]
intron_size_downstream_template[ , `:=`(exon_pos="downstream", strand="template") ]
intron_size_TOTAL <- rbind(intron_size_upstream_non_template, intron_size_downstream_non_template, intron_size_upstream_template, intron_size_downstream_template )
colnames(intron_size_TOTAL) <- c("chrom", "start", "end", "strand", "intron_number", "intron_size", "Transcript", "G4", "exon_pos", "Strand" )
Here we explored how G4 enrichments change thorugh gene body
exons_1.up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_1_plus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_1_plus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_1.down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_1_plus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_1_plus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_1.up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_1_minus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_1_minus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_1.down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_1_minus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_1_minus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_1.up_minus[,Position:=Position*-1]
exons_1.down_minus[,Position:=Position*-1]
exons_1.TOTAL <- plot_density(exons_1.up_plus, exons_1.up_minus, exons_1.down_plus, exons_1.down_minus)
exons_2.up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_2_plus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_2_plus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_2.down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_2_plus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_2_plus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_2.up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_2_minus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_2_minus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_2.down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_2_minus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_2_minus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_2.up_minus[,Position:=Position*-1]
exons_2.down_minus[,Position:=Position*-1]
exons_2.TOTAL <- plot_density(exons_2.up_plus, exons_2.up_minus, exons_2.down_plus, exons_2.down_minus)
exons_3.up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_3_plus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_3_plus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_3.down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_3_plus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_3_plus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_3.up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_3_minus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_3_minus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_3.down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_3_minus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_3_minus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_3.up_minus[,Position:=Position*-1]
exons_3.down_minus[,Position:=Position*-1]
exons_3.TOTAL <- plot_density(exons_3.up_plus, exons_3.up_minus, exons_3.down_plus, exons_3.down_minus)
exons_4.up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_4_plus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_4_plus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_4.down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_4_plus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_4_plus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_4.up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_4_minus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_4_minus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_4.down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_4_minus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_4_minus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_4.up_minus[,Position:=Position*-1]
exons_4.down_minus[,Position:=Position*-1]
exons_4.TOTAL <- plot_density(exons_4.up_plus, exons_4.up_minus, exons_4.down_plus, exons_4.down_minus)
exons_middle.up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_middle_plus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_middle_plus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_middle.down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_middle_plus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_middle_plus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_middle.up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_middle_minus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_middle_minus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_middle.down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_middle_minus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_middle_minus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_middle.up_minus[,Position:=Position*-1]
exons_middle.down_minus[,Position:=Position*-1]
exons_middle.TOTAL <- plot_density(exons_middle.up_plus, exons_middle.up_minus, exons_middle.down_plus, exons_middle.down_minus)
exons_minus4.up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus4_plus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus4_plus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_minus4.down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus4_plus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus4_plus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_minus4.up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus4_minus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus4_minus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_minus4.down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus4_minus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus4_minus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_minus4.up_minus[,Position:=Position*-1]
exons_minus4.down_minus[,Position:=Position*-1]
exons_minus4.TOTAL <- plot_density(exons_minus4.up_plus, exons_minus4.up_minus, exons_minus4.down_plus, exons_minus4.down_minus)
exons_minus3.up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus3_plus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus3_plus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_minus3.down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus3_plus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus3_plus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_minus3.up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus3_minus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus3_minus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_minus3.down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus3_minus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus3_minus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_minus3.up_minus[,Position:=Position*-1]
exons_minus3.down_minus[,Position:=Position*-1]
exons_minus3.TOTAL <- plot_density(exons_minus3.up_plus, exons_minus3.up_minus, exons_minus3.down_plus, exons_minus3.down_minus)
exons_minus2.up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus2_plus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus2_plus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_minus2.down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus2_plus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus2_plus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_minus2.up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus2_minus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus2_minus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_minus2.down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus2_minus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus2_minus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_minus2.up_minus[,Position:=Position*-1]
exons_minus2.down_minus[,Position:=Position*-1]
exons_minus2.TOTAL <- plot_density(exons_minus2.up_plus, exons_minus2.up_minus, exons_minus2.down_plus, exons_minus2.down_minus)
exons_minus1.up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus1_plus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus1_plus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_minus1.down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus1_plus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus1_plus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_minus1.up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus1_minus_strand_upstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus1_minus_strand_upstream.txt.score.G4.bed.list.out.num'
exons_minus1.down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus1_minus_strand_downstream.txt.score.G4.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/exon_numbers/exons_minus1_minus_strand_downstream.txt.score.G4.bed.list.out.num'
exons_minus1.up_minus[,Position:=Position*-1]
exons_minus1.down_minus[,Position:=Position*-1]
exons_minus1.TOTAL <- plot_density(exons_minus1.up_plus, exons_minus1.up_minus, exons_minus1.down_plus, exons_minus1.down_minus)
exons_1.TOTAL[, exon_num:="1"]
exons_2.TOTAL[, exon_num:="2"]
exons_3.TOTAL[, exon_num:="3"]
exons_4.TOTAL[, exon_num:="4"]
exons_middle.TOTAL[, exon_num:="middle"]
exons_minus4.TOTAL[, exon_num:="-4"]
exons_minus3.TOTAL[, exon_num:="-3"]
exons_minus2.TOTAL[, exon_num:="-2"]
exons_minus1.TOTAL[, exon_num:="-1"]
exon_num.TOTAL <- rbind(exons_1.TOTAL, exons_2.TOTAL, exons_3.TOTAL, exons_4.TOTAL, exons_middle.TOTAL, exons_minus4.TOTAL, exons_minus3.TOTAL, exons_minus2.TOTAL, exons_minus1.TOTAL)
exon_num.TOTAL$exon_num <- factor(exon_num.TOTAL$exon_num, levels = c("1", "2", "3", "4", "middle", "-4", "-3", "-2", "-1" ))
ggplot(exon_num.TOTAL)+
geom_line(aes(x=Position,y=Enrrichment)) +
xlim(c(-300,300)) +
facet_grid( exon_pos ~ exon_num ) +
theme_bw()
Here we distribution of G4-seq experiments
G4_2019.K.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.K.Qs.plus.up.list <- list(G4_2019.K.Q1_up_plus, G4_2019.K.Q2_up_plus, G4_2019.K.Q3_up_plus, G4_2019.K.Q4_up_plus)
G4_2019.K.Qs.minus.list <- list(G4_2019.K.Q1_up_minus, G4_2019.K.Q2_up_minus, G4_2019.K.Q3_up_minus, G4_2019.K.Q4_up_minus)
G4_2019.K.Qs.plus.down.list <- list(G4_2019.K.Q1_down_plus, G4_2019.K.Q2_down_plus, G4_2019.K.Q3_down_plus, G4_2019.K.Q4_down_plus)
G4_2019.K.Qs.minus.down.list <- list(G4_2019.K.Q1_down_minus, G4_2019.K.Q2_down_minus, G4_2019.K.Q3_down_minus, G4_2019.K.Q4_down_minus)
G4_2019.K.window_len = 2000
G4_2019.K.Qs.total <- get_total_Qs(G4_2019.K.Qs.plus.up.list, G4_2019.K.Qs.minus.list, G4_2019.K.Qs.plus.down.list, G4_2019.K.Qs.minus.down.list, G4_2019.K.window_len)
ggplot(G4_2019.K.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-200,200)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw() +
labs(colour = "Splice site stregth quartile") +
theme(legend.position = "top", legend.direction = "horizontal")
G4_2019.PDS.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.PDS.Qs.plus.up.list <- list(G4_2019.PDS.Q1_up_plus, G4_2019.PDS.Q2_up_plus, G4_2019.PDS.Q3_up_plus, G4_2019.PDS.Q4_up_plus)
G4_2019.PDS.Qs.minus.list <- list(G4_2019.PDS.Q1_up_minus, G4_2019.PDS.Q2_up_minus, G4_2019.PDS.Q3_up_minus, G4_2019.PDS.Q4_up_minus)
G4_2019.PDS.Qs.plus.down.list <- list(G4_2019.PDS.Q1_down_plus, G4_2019.PDS.Q2_down_plus, G4_2019.PDS.Q3_down_plus, G4_2019.PDS.Q4_down_plus)
G4_2019.PDS.Qs.minus.down.list <- list(G4_2019.PDS.Q1_down_minus, G4_2019.PDS.Q2_down_minus, G4_2019.PDS.Q3_down_minus, G4_2019.PDS.Q4_down_minus)
G4_2019.PDS.window_len = 2000
G4_2019.PDS.Qs.total <- get_total_Qs(G4_2019.PDS.Qs.plus.up.list, G4_2019.PDS.Qs.minus.list, G4_2019.PDS.Qs.plus.down.list, G4_2019.PDS.Qs.minus.down.list, G4_2019.PDS.window_len)
ggplot(G4_2019.PDS.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-200,200)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw() +
labs(colour = "Splice site stregth quartile") +
theme(legend.position = "top", legend.direction = "horizontal")
G4_2019.template.PDS.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.non_template.PDS.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.bed.list.out.num'
G4_2019.template.PDS.Qs.plus.up.list <- list(G4_2019.template.PDS.Q1_up_plus, G4_2019.template.PDS.Q2_up_plus, G4_2019.template.PDS.Q3_up_plus, G4_2019.template.PDS.Q4_up_plus)
G4_2019.template.PDS.Qs.minus.list <- list(G4_2019.template.PDS.Q1_up_minus, G4_2019.template.PDS.Q2_up_minus, G4_2019.template.PDS.Q3_up_minus, G4_2019.template.PDS.Q4_up_minus)
G4_2019.template.PDS.Qs.plus.down.list <- list(G4_2019.template.PDS.Q1_down_plus, G4_2019.template.PDS.Q2_down_plus, G4_2019.template.PDS.Q3_down_plus, G4_2019.template.PDS.Q4_down_plus)
G4_2019.template.PDS.Qs.minus.down.list <- list(G4_2019.template.PDS.Q1_down_minus, G4_2019.template.PDS.Q2_down_minus, G4_2019.template.PDS.Q3_down_minus, G4_2019.template.PDS.Q4_down_minus)
G4_2019.template.PDS.window_len = 2000
G4_2019.template.PDS.Qs.total <- get_total_Qs(G4_2019.template.PDS.Qs.plus.up.list, G4_2019.template.PDS.Qs.minus.list, G4_2019.template.PDS.Qs.plus.down.list, G4_2019.template.PDS.Qs.minus.down.list, window_len)
G4_2019.non_template.PDS.Qs.plus.up.list <- list(G4_2019.non_template.PDS.Q1_up_plus, G4_2019.non_template.PDS.Q2_up_plus, G4_2019.non_template.PDS.Q3_up_plus, G4_2019.non_template.PDS.Q4_up_plus)
G4_2019.non_template.PDS.Qs.minus.list <- list(G4_2019.non_template.PDS.Q1_up_minus, G4_2019.non_template.PDS.Q2_up_minus, G4_2019.non_template.PDS.Q3_up_minus, G4_2019.non_template.PDS.Q4_up_minus)
G4_2019.non_template.PDS.Qs.plus.down.list <- list(G4_2019.non_template.PDS.Q1_down_plus, G4_2019.non_template.PDS.Q2_down_plus, G4_2019.non_template.PDS.Q3_down_plus, G4_2019.non_template.PDS.Q4_down_plus)
G4_2019.non_template.PDS.Qs.minus.down.list <- list(G4_2019.non_template.PDS.Q1_down_minus, G4_2019.non_template.PDS.Q2_down_minus, G4_2019.non_template.PDS.Q3_down_minus, G4_2019.non_template.PDS.Q4_down_minus)
G4_2019.non_template.PDS.window_len = 2000
G4_2019.non_template.PDS.Qs.total <- get_total_Qs(G4_2019.non_template.PDS.Qs.plus.up.list, G4_2019.non_template.PDS.Qs.minus.list, G4_2019.non_template.PDS.Qs.plus.down.list, G4_2019.non_template.PDS.Qs.minus.down.list, window_len)
G4_2019.template_non_template.PDS.Qs.total <- rbind(G4_2019.template.PDS.Qs.total, G4_2019.non_template.PDS.Qs.total)
half_n <- nrow(G4_2019.template_non_template.PDS.Qs.total)/2
G4_2019.template_non_template.PDS.Qs.total[, Strand:=rep(c("Template", "Non-template"), each=half_n) ]
G4_2019.template_non_template.PDS.Qs.total$Strand <- factor(G4_2019.template_non_template.PDS.Qs.total$Strand, levels=c("Template", "Non-template" ))
G4_2019.template_non_template.PDS.Qs.total$Q <- mapvalues(G4_2019.template_non_template.PDS.Qs.total$Q, from =c(1:4), to =c("Q1", "Q2", "Q3", "Q4"))
ggplot(G4_2019.template_non_template.PDS.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-150,150)) +
facet_grid( Strand ~ exon_pos ) +
labs(colour = "Splice site stregth quartile") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
G4_2019.template_non_template.PDS.Qs.total[Strand=="Non-template" , new_Strand:="Template"]
G4_2019.template_non_template.PDS.Qs.total[Strand=="Template" , new_Strand:="Non-template"]
G4_2019.template_non_template.PDS.Qs.total$new_Strand <- factor(G4_2019.template_non_template.PDS.Qs.total$new_Strand, levels=c("Template", "Non-template" ))
ggplot(G4_2019.template_non_template.PDS.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-150,150)) +
facet_grid( new_Strand ~ exon_pos ) +
labs(colour = "Splice site stregth quartile") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
G4_2019.template.K.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.up_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_plus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q1.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q2.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q3.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.non_template.K.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2019/exon.down_minus.q4.bed.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.bed.list.out.num'
G4_2019.template.K.Qs.plus.up.list <- list(G4_2019.template.K.Q1_up_plus, G4_2019.template.K.Q2_up_plus, G4_2019.template.K.Q3_up_plus, G4_2019.template.K.Q4_up_plus)
G4_2019.template.K.Qs.minus.list <- list(G4_2019.template.K.Q1_up_minus, G4_2019.template.K.Q2_up_minus, G4_2019.template.K.Q3_up_minus, G4_2019.template.K.Q4_up_minus)
G4_2019.template.K.Qs.plus.down.list <- list(G4_2019.template.K.Q1_down_plus, G4_2019.template.K.Q2_down_plus, G4_2019.template.K.Q3_down_plus, G4_2019.template.K.Q4_down_plus)
G4_2019.template.K.Qs.minus.down.list <- list(G4_2019.template.K.Q1_down_minus, G4_2019.template.K.Q2_down_minus, G4_2019.template.K.Q3_down_minus, G4_2019.template.K.Q4_down_minus)
G4_2019.template.K.window_len = 2000
G4_2019.template.K.Qs.total <- get_total_Qs(G4_2019.template.K.Qs.plus.up.list, G4_2019.template.K.Qs.minus.list, G4_2019.template.K.Qs.plus.down.list, G4_2019.template.K.Qs.minus.down.list, window_len)
G4_2019.non_template.K.Qs.plus.up.list <- list(G4_2019.non_template.K.Q1_up_plus, G4_2019.non_template.K.Q2_up_plus, G4_2019.non_template.K.Q3_up_plus, G4_2019.non_template.K.Q4_up_plus)
G4_2019.non_template.K.Qs.minus.list <- list(G4_2019.non_template.K.Q1_up_minus, G4_2019.non_template.K.Q2_up_minus, G4_2019.non_template.K.Q3_up_minus, G4_2019.non_template.K.Q4_up_minus)
G4_2019.non_template.K.Qs.plus.down.list <- list(G4_2019.non_template.K.Q1_down_plus, G4_2019.non_template.K.Q2_down_plus, G4_2019.non_template.K.Q3_down_plus, G4_2019.non_template.K.Q4_down_plus)
G4_2019.non_template.K.Qs.minus.down.list <- list(G4_2019.non_template.K.Q1_down_minus, G4_2019.non_template.K.Q2_down_minus, G4_2019.non_template.K.Q3_down_minus, G4_2019.non_template.K.Q4_down_minus)
G4_2019.non_template.K.window_len = 2000
G4_2019.non_template.K.Qs.total <- get_total_Qs(G4_2019.non_template.K.Qs.plus.up.list, G4_2019.non_template.K.Qs.minus.list, G4_2019.non_template.K.Qs.plus.down.list, G4_2019.non_template.K.Qs.minus.down.list, window_len)
G4_2019.template.K.Qs.total
Position Q Occurrences.x median.x Enrrichment.x Occurrences.y median.y Enrrichment.y Occurrences median Enrrichment exon_pos
1: -1000 1 825 903.0 0.9136213 840 854 0.9836066 1665 1741 0.9563469 Upstream
2: -1000 2 673 716.0 0.9399441 638 684 0.9327485 1311 1408 0.9311080 Upstream
3: -1000 3 555 567.0 0.9788360 592 546 1.0842491 1147 1116 1.0277778 Upstream
4: -1000 4 413 370.0 1.1162162 364 370 0.9837838 777 749 1.0373832 Upstream
5: -999 1 833 903.0 0.9224806 845 854 0.9894614 1678 1741 0.9638139 Upstream
---
15988: 997 4 480 540.0 0.8888889 474 540 0.8777778 954 1093 0.8728271 Downstream
15989: 998 1 579 698.0 0.8295129 561 640 0.8765625 1140 1347 0.8463252 Downstream
15990: 998 2 560 680.0 0.8235294 527 657 0.8021309 1087 1334 0.8148426 Downstream
15991: 998 3 504 590.5 0.8535140 472 595 0.7932773 976 1192 0.8187919 Downstream
15992: 998 4 484 540.0 0.8962963 474 540 0.8777778 958 1093 0.8764867 Downstream
G4_2019.non_template.K.Qs.total
Position Q Occurrences.x median.x Enrrichment.x Occurrences.y median.y Enrrichment.y Occurrences median Enrrichment exon_pos
1: -1000 1 682 749 0.9105474 697 726 0.9600551 1379 1471 0.9374575 Upstream
2: -1000 2 564 618 0.9126214 573 594 0.9646465 1137 1212 0.9381188 Upstream
3: -1000 3 455 469 0.9701493 455 450 1.0111111 910 920 0.9891304 Upstream
4: -1000 4 339 341 0.9941349 345 324 1.0648148 684 665 1.0285714 Upstream
5: -999 1 685 749 0.9145527 695 726 0.9573003 1380 1471 0.9381373 Upstream
---
15988: 997 4 475 505 0.9405941 453 471 0.9617834 928 969 0.9576883 Downstream
15989: 998 1 614 600 1.0233333 494 558 0.8853047 1108 1151 0.9626412 Downstream
15990: 998 2 553 567 0.9753086 542 548 0.9890511 1095 1113 0.9838275 Downstream
15991: 998 3 530 523 1.0133843 461 494 0.9331984 991 1014 0.9773176 Downstream
15992: 998 4 474 505 0.9386139 456 471 0.9681529 930 969 0.9597523 Downstream
G4_2019.template_non_template.K.Qs.total <- rbind(G4_2019.template.K.Qs.total, G4_2019.non_template.K.Qs.total)
half_n <- nrow(G4_2019.template_non_template.K.Qs.total)/2
G4_2019.template_non_template.K.Qs.total[, Strand:=rep(c("Template", "Non-template"), each=half_n) ]
G4_2019.template_non_template.K.Qs.total$Strand <- factor(G4_2019.template_non_template.K.Qs.total$Strand, levels=c("Template", "Non-template" ))
G4_2019.template_non_template.K.Qs.total$Q <- mapvalues(G4_2019.template_non_template.K.Qs.total$Q, from =c(1:4), to =c("Q1", "Q2", "Q3", "Q4"))
G4_2019.template_non_template.K.Qs.total[Strand=="Non-template" , new_Strand:="Template"]
G4_2019.template_non_template.K.Qs.total[Strand=="Template" , new_Strand:="Non-template"]
G4_2019.template_non_template.K.Qs.total$new_Strand <- factor(G4_2019.template_non_template.K.Qs.total$new_Strand, levels=c("Template", "Non-template" ))
ggplot(G4_2019.template_non_template.K.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-150,150)) +
facet_grid( new_Strand ~ exon_pos ) +
labs(colour = "Splice site stregth quartile") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
#2015
G4_2015.Na_PDS.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_PDS_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_PDS.Qs.plus.up.list <- list(G4_2015.Na_PDS.Q1_up_plus, G4_2015.Na_PDS.Q2_up_plus, G4_2015.Na_PDS.Q3_up_plus, G4_2015.Na_PDS.Q4_up_plus)
G4_2015.Na_PDS.Qs.minus.list <- list(G4_2015.Na_PDS.Q1_up_minus, G4_2015.Na_PDS.Q2_up_minus, G4_2015.Na_PDS.Q3_up_minus, G4_2015.Na_PDS.Q4_up_minus)
G4_2015.Na_PDS.Qs.plus.down.list <- list(G4_2015.Na_PDS.Q1_down_plus, G4_2015.Na_PDS.Q2_down_plus, G4_2015.Na_PDS.Q3_down_plus, G4_2015.Na_PDS.Q4_down_plus)
G4_2015.Na_PDS.Qs.minus.down.list <- list(G4_2015.Na_PDS.Q1_down_minus, G4_2015.Na_PDS.Q2_down_minus, G4_2015.Na_PDS.Q3_down_minus, G4_2015.Na_PDS.Q4_down_minus)
G4_2015.Na_PDS.window_len = 2000
G4_2015.Na_PDS.Qs.total <- get_total_Qs(G4_2015.Na_PDS.Qs.plus.up.list, G4_2015.Na_PDS.Qs.minus.list, G4_2015.Na_PDS.Qs.plus.down.list, G4_2015.Na_PDS.Qs.minus.down.list, G4_2015.Na_PDS.window_len)
ggplot(G4_2015.Na_PDS.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-200,200)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw() +
labs(colour = "Splice site stregth quartile") +
theme(legend.position = "top", legend.direction = "horizontal")
G4_2015.Na_K.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_K_plus_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.Na_K.Qs.plus.up.list <- list(G4_2015.Na_K.Q1_up_plus, G4_2015.Na_K.Q2_up_plus, G4_2015.Na_K.Q3_up_plus, G4_2015.Na_K.Q4_up_plus)
G4_2015.Na_K.Qs.minus.list <- list(G4_2015.Na_K.Q1_up_minus, G4_2015.Na_K.Q2_up_minus, G4_2015.Na_K.Q3_up_minus, G4_2015.Na_K.Q4_up_minus)
G4_2015.Na_K.Qs.plus.down.list <- list(G4_2015.Na_K.Q1_down_plus, G4_2015.Na_K.Q2_down_plus, G4_2015.Na_K.Q3_down_plus, G4_2015.Na_K.Q4_down_plus)
G4_2015.Na_K.Qs.minus.down.list <- list(G4_2015.Na_K.Q1_down_minus, G4_2015.Na_K.Q2_down_minus, G4_2015.Na_K.Q3_down_minus, G4_2015.Na_K.Q4_down_minus)
G4_2015.Na_K.window_len = 2000
G4_2015.Na_K.Qs.total <- get_total_Qs(G4_2015.Na_K.Qs.plus.up.list, G4_2015.Na_K.Qs.minus.list, G4_2015.Na_K.Qs.plus.down.list, G4_2015.Na_K.Qs.minus.down.list, G4_2015.Na_K.window_len)
ggplot(G4_2015.Na_K.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-200,200)) +
facet_grid( . ~ exon_pos ) +
theme(text = element_text(size=15)) +
theme_bw() +
labs(colour = "Splice site stregth quartile") +
theme(legend.position = "top", legend.direction = "horizontal")
G4_2015.template.Na_PDS.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_PDS_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_PDS.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_PDS_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_PDS.Qs.plus.up.list <- list(G4_2015.template.Na_PDS.Q1_up_plus, G4_2015.template.Na_PDS.Q2_up_plus, G4_2015.template.Na_PDS.Q3_up_plus, G4_2015.template.Na_PDS.Q4_up_plus)
G4_2015.template.Na_PDS.Qs.minus.list <- list(G4_2015.template.Na_PDS.Q1_up_minus, G4_2015.template.Na_PDS.Q2_up_minus, G4_2015.template.Na_PDS.Q3_up_minus, G4_2015.template.Na_PDS.Q4_up_minus)
G4_2015.template.Na_PDS.Qs.plus.down.list <- list(G4_2015.template.Na_PDS.Q1_down_plus, G4_2015.template.Na_PDS.Q2_down_plus, G4_2015.template.Na_PDS.Q3_down_plus, G4_2015.template.Na_PDS.Q4_down_plus)
G4_2015.template.Na_PDS.Qs.minus.down.list <- list(G4_2015.template.Na_PDS.Q1_down_minus, G4_2015.template.Na_PDS.Q2_down_minus, G4_2015.template.Na_PDS.Q3_down_minus, G4_2015.template.Na_PDS.Q4_down_minus)
G4_2015.template.Na_PDS.window_len = 2000
G4_2015.template.Na_PDS.Qs.total <- get_total_Qs(G4_2015.template.Na_PDS.Qs.plus.up.list, G4_2015.template.Na_PDS.Qs.minus.list, G4_2015.template.Na_PDS.Qs.plus.down.list, G4_2015.template.Na_PDS.Qs.minus.down.list, window_len)
G4_2015.non_template.Na_PDS.Qs.plus.up.list <- list(G4_2015.non_template.Na_PDS.Q1_up_plus, G4_2015.non_template.Na_PDS.Q2_up_plus, G4_2015.non_template.Na_PDS.Q3_up_plus, G4_2015.non_template.Na_PDS.Q4_up_plus)
G4_2015.non_template.Na_PDS.Qs.minus.list <- list(G4_2015.non_template.Na_PDS.Q1_up_minus, G4_2015.non_template.Na_PDS.Q2_up_minus, G4_2015.non_template.Na_PDS.Q3_up_minus, G4_2015.non_template.Na_PDS.Q4_up_minus)
G4_2015.non_template.Na_PDS.Qs.plus.down.list <- list(G4_2015.non_template.Na_PDS.Q1_down_plus, G4_2015.non_template.Na_PDS.Q2_down_plus, G4_2015.non_template.Na_PDS.Q3_down_plus, G4_2015.non_template.Na_PDS.Q4_down_plus)
G4_2015.non_template.Na_PDS.Qs.minus.down.list <- list(G4_2015.non_template.Na_PDS.Q1_down_minus, G4_2015.non_template.Na_PDS.Q2_down_minus, G4_2015.non_template.Na_PDS.Q3_down_minus, G4_2015.non_template.Na_PDS.Q4_down_minus)
G4_2015.non_template.Na_PDS.window_len = 2000
G4_2015.non_template.Na_PDS.Qs.total <- get_total_Qs(G4_2015.non_template.Na_PDS.Qs.plus.up.list, G4_2015.non_template.Na_PDS.Qs.minus.list, G4_2015.non_template.Na_PDS.Qs.plus.down.list, G4_2015.non_template.Na_PDS.Qs.minus.down.list, window_len)
G4_2015.template.Na_PDS.Qs.total
Position Q Occurrences.x median.x Enrrichment.x Occurrences.y median.y Enrrichment.y Occurrences median Enrrichment exon_pos
1: -1000 1 3230 3421 0.9441684 3119 3238.5 0.9631002 6349 6677 0.9508761 Upstream
2: -1000 2 2693 2711 0.9933604 2396 2540.0 0.9433071 5089 5232 0.9726682 Upstream
3: -1000 3 1991 1997 0.9969955 1927 1975.0 0.9756962 3918 3998 0.9799900 Upstream
4: -1000 4 1455 1331 1.0931630 1357 1287.0 1.0543901 2812 2635 1.0671727 Upstream
5: -999 1 3244 3421 0.9482607 3112 3238.5 0.9609387 6356 6677 0.9519245 Upstream
---
15988: 997 4 1716 2058 0.8338192 1686 2051.0 0.8220380 3402 4144 0.8209459 Downstream
15989: 998 1 2169 2586 0.8387471 2143 2386.0 0.8981559 4312 4961 0.8691796 Downstream
15990: 998 2 2130 2578 0.8262219 1926 2395.0 0.8041754 4056 4983 0.8139675 Downstream
15991: 998 3 1854 2200 0.8427273 1865 2153.0 0.8662332 3719 4357 0.8535690 Downstream
15992: 998 4 1716 2058 0.8338192 1684 2051.0 0.8210629 3400 4144 0.8204633 Downstream
G4_2015.non_template.Na_PDS.Qs.total
Position Q Occurrences.x median.x Enrrichment.x Occurrences.y median.y Enrrichment.y Occurrences median Enrrichment exon_pos
1: -1000 1 2746 2794.0 0.9828203 2528 2744.0 0.9212828 5274 5538 0.9523294 Upstream
2: -1000 2 2178 2259.0 0.9641434 1987 2130.0 0.9328638 4165 4378 0.9513476 Upstream
3: -1000 3 1591 1697.0 0.9375368 1566 1590.0 0.9849057 3157 3266 0.9666258 Upstream
4: -1000 4 1190 1162.0 1.0240964 1095 1068.0 1.0252809 2285 2223 1.0278902 Upstream
5: -999 1 2736 2794.0 0.9792412 2533 2744.0 0.9231050 5269 5538 0.9514265 Upstream
---
15988: 997 4 1671 1744.0 0.9581422 1540 1686.0 0.9134045 3211 3394 0.9460813 Downstream
15989: 998 1 2109 2196.0 0.9603825 1862 2021.0 0.9213261 3971 4204 0.9445766 Downstream
15990: 998 2 1996 2118.5 0.9421761 1846 2024.5 0.9118301 3842 4140 0.9280193 Downstream
15991: 998 3 1793 1857.0 0.9655358 1733 1799.0 0.9633130 3526 3665 0.9620737 Downstream
15992: 998 4 1672 1744.0 0.9587156 1545 1686.0 0.9163701 3217 3394 0.9478491 Downstream
G4_2015.template_non_template.Na_PDS.Qs.total <- rbind(G4_2015.template.Na_PDS.Qs.total, G4_2015.non_template.Na_PDS.Qs.total)
half_n <- nrow(G4_2015.template_non_template.Na_PDS.Qs.total)/2
G4_2015.template_non_template.Na_PDS.Qs.total[, Strand:=rep(c("Template", "Non-template"), each=half_n) ]
G4_2015.template_non_template.Na_PDS.Qs.total$Strand <- factor(G4_2015.template_non_template.Na_PDS.Qs.total$Strand, levels=c("Template", "Non-template" ))
G4_2015.template_non_template.Na_PDS.Qs.total$Q <- mapvalues(G4_2015.template_non_template.Na_PDS.Qs.total$Q, from =c(1:4), to =c("Q1", "Q2", "Q3", "Q4"))
G4_2015.template_non_template.Na_PDS.Qs.total[Strand=="Non-template" , new_Strand:="Template"]
G4_2015.template_non_template.Na_PDS.Qs.total[Strand=="Template" , new_Strand:="Non-template"]
G4_2015.template_non_template.Na_PDS.Qs.total$new_Strand <- factor(G4_2015.template_non_template.Na_PDS.Qs.total$new_Strand, levels=c("Template", "Non-template" ))
ggplot(G4_2015.template_non_template.Na_PDS.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-300,300)) +
facet_grid( new_Strand ~ exon_pos ) +
labs(colour = "Splice site stregth quartile") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
G4_2015.template.Na_K.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q1_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q1.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q2_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q2.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q3_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q3.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q4_up_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_plus.q4.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q1_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q1.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q2_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q2.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q3_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q3.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q4_up_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.up_minus.q4.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q1_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q1.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q2_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q2.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q3_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q3.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q4_down_plus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_plus.q4.bed.score.GSE63874_Na_K_plus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q1_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q1.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q2_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q2.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q3_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q3.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.non_template.Na_K.Q4_down_minus <- read_dist_table("/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '/Users/gp7/Google_Drive/Results/Non_B/G4_seq_2015/exon.down_minus.q4.bed.score.GSE63874_Na_K_minus_hits_intersect.bed.bed.list.out.num'
G4_2015.template.Na_K.Qs.plus.up.list <- list(G4_2015.template.Na_K.Q1_up_plus, G4_2015.template.Na_K.Q2_up_plus, G4_2015.template.Na_K.Q3_up_plus, G4_2015.template.Na_K.Q4_up_plus)
G4_2015.template.Na_K.Qs.minus.list <- list(G4_2015.template.Na_K.Q1_up_minus, G4_2015.template.Na_K.Q2_up_minus, G4_2015.template.Na_K.Q3_up_minus, G4_2015.template.Na_K.Q4_up_minus)
G4_2015.template.Na_K.Qs.plus.down.list <- list(G4_2015.template.Na_K.Q1_down_plus, G4_2015.template.Na_K.Q2_down_plus, G4_2015.template.Na_K.Q3_down_plus, G4_2015.template.Na_K.Q4_down_plus)
G4_2015.template.Na_K.Qs.minus.down.list <- list(G4_2015.template.Na_K.Q1_down_minus, G4_2015.template.Na_K.Q2_down_minus, G4_2015.template.Na_K.Q3_down_minus, G4_2015.template.Na_K.Q4_down_minus)
G4_2015.template.Na_K.window_len = 2000
G4_2015.template.Na_K.Qs.total <- get_total_Qs(G4_2015.template.Na_K.Qs.plus.up.list, G4_2015.template.Na_K.Qs.minus.list, G4_2015.template.Na_K.Qs.plus.down.list, G4_2015.template.Na_K.Qs.minus.down.list, window_len)
G4_2015.non_template.Na_K.Qs.plus.up.list <- list(G4_2015.non_template.Na_K.Q1_up_plus, G4_2015.non_template.Na_K.Q2_up_plus, G4_2015.non_template.Na_K.Q3_up_plus, G4_2015.non_template.Na_K.Q4_up_plus)
G4_2015.non_template.Na_K.Qs.minus.list <- list(G4_2015.non_template.Na_K.Q1_up_minus, G4_2015.non_template.Na_K.Q2_up_minus, G4_2015.non_template.Na_K.Q3_up_minus, G4_2015.non_template.Na_K.Q4_up_minus)
G4_2015.non_template.Na_K.Qs.plus.down.list <- list(G4_2015.non_template.Na_K.Q1_down_plus, G4_2015.non_template.Na_K.Q2_down_plus, G4_2015.non_template.Na_K.Q3_down_plus, G4_2015.non_template.Na_K.Q4_down_plus)
G4_2015.non_template.Na_K.Qs.minus.down.list <- list(G4_2015.non_template.Na_K.Q1_down_minus, G4_2015.non_template.Na_K.Q2_down_minus, G4_2015.non_template.Na_K.Q3_down_minus, G4_2015.non_template.Na_K.Q4_down_minus)
G4_2015.non_template.Na_K.window_len = 2000
G4_2015.non_template.Na_K.Qs.total <- get_total_Qs(G4_2015.non_template.Na_K.Qs.plus.up.list, G4_2015.non_template.Na_K.Qs.minus.list, G4_2015.non_template.Na_K.Qs.plus.down.list, G4_2015.non_template.Na_K.Qs.minus.down.list, window_len)
G4_2015.template.Na_K.Qs.total
Position Q Occurrences.x median.x Enrrichment.x Occurrences.y median.y Enrrichment.y Occurrences median Enrrichment exon_pos
1: -1000 1 2362 2490.0 0.9485944 2292 2412.0 0.9502488 4654 4893 0.9511547 Upstream
2: -1000 2 1928 1952.0 0.9877049 1753 1901.0 0.9221462 3681 3861 0.9533800 Upstream
3: -1000 3 1549 1514.0 1.0231176 1497 1471.0 1.0176751 3046 2984 1.0207775 Upstream
4: -1000 4 1099 1038.0 1.0587669 1074 1000.0 1.0740000 2173 2036 1.0672888 Upstream
5: -999 1 2356 2490.0 0.9461847 2299 2412.0 0.9531509 4655 4893 0.9513591 Upstream
---
15988: 997 4 1294 1470.5 0.8799728 1309 1463.5 0.8944312 2603 2934 0.8871847 Downstream
15989: 998 1 1609 1914.0 0.8406479 1565 1797.0 0.8708959 3174 3710 0.8555256 Downstream
15990: 998 2 1556 1874.0 0.8303095 1486 1786.0 0.8320269 3042 3657 0.8318294 Downstream
15991: 998 3 1403 1633.0 0.8591549 1386 1618.0 0.8566131 2789 3265 0.8542113 Downstream
15992: 998 4 1294 1470.5 0.8799728 1305 1463.5 0.8916980 2599 2934 0.8858214 Downstream
G4_2015.non_template.Na_K.Qs.total
Position Q Occurrences.x median.x Enrrichment.x Occurrences.y median.y Enrrichment.y Occurrences median Enrrichment exon_pos
1: -1000 1 1927 2021.0 0.9534884 1792 1970.5 0.9094139 3719 3995 0.9309136 Upstream
2: -1000 2 1575 1674.5 0.9405793 1500 1575.5 0.9520787 3075 3242 0.9484886 Upstream
3: -1000 3 1265 1280.0 0.9882812 1183 1197.0 0.9883041 2448 2474 0.9894907 Upstream
4: -1000 4 930 926.0 1.0043197 870 852.0 1.0211268 1800 1765 1.0198300 Upstream
5: -999 1 1924 2021.0 0.9520040 1795 1970.5 0.9109363 3719 3995 0.9309136 Upstream
---
15988: 997 4 1320 1303.0 1.0130468 1142 1275.0 0.8956863 2462 2566 0.9594700 Downstream
15989: 998 1 1569 1623.0 0.9667283 1369 1523.5 0.8985888 2938 3121 0.9413649 Downstream
15990: 998 2 1468 1579.0 0.9297023 1422 1466.0 0.9699864 2890 3039 0.9509707 Downstream
15991: 998 3 1368 1408.0 0.9715909 1280 1327.0 0.9645818 2648 2734 0.9685443 Downstream
15992: 998 4 1319 1303.0 1.0122794 1145 1275.0 0.8980392 2464 2566 0.9602494 Downstream
G4_2015.template_non_template.Na_K.Qs.total <- rbind(G4_2015.template.Na_K.Qs.total, G4_2015.non_template.Na_K.Qs.total)
half_n <- nrow(G4_2015.template_non_template.Na_K.Qs.total)/2
G4_2015.template_non_template.Na_K.Qs.total[, Strand:=rep(c("Template", "Non-template"), each=half_n) ]
G4_2015.template_non_template.Na_K.Qs.total$Strand <- factor(G4_2015.template_non_template.Na_K.Qs.total$Strand, levels=c("Template", "Non-template" ))
G4_2015.template_non_template.Na_K.Qs.total$Q <- mapvalues(G4_2015.template_non_template.Na_K.Qs.total$Q, from =c(1:4), to =c("Q1", "Q2", "Q3", "Q4"))
G4_2015.template_non_template.Na_K.Qs.total[Strand=="Non-template" , new_Strand:="Template"]
G4_2015.template_non_template.Na_K.Qs.total[Strand=="Template" , new_Strand:="Non-template"]
G4_2015.template_non_template.Na_K.Qs.total$new_Strand <- factor(G4_2015.template_non_template.Na_K.Qs.total$new_Strand, levels=c("Template", "Non-template" ))
ggplot(G4_2015.template_non_template.Na_K.Qs.total)+
geom_line(aes(x=Position,y=Enrrichment, colour=Q)) +
xlim(c(-300,300)) +
facet_grid( new_Strand ~ exon_pos ) +
labs(colour = "Splice site stregth quartile") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
As K+ is known to stabilize G4, we analized (RNA-seq data)[https://www.ncbi.nlm.nih.gov/bioproject/PRJEB19451] comming from neurons after 4-hour KCl-indused depolarization.
KCL_human_upstream <- fread("./KCL/MicroExonator/Control_vs_KCL.diff.upstream_100nt.G4s" )
colnames(KCL_human_upstream) <- c("w.chrom", "w.start", "w.end", "w.strand", "chrom", "start", "end", "strand", "Type", "Psi_A", "Psi_B", "DeltaPsi", "Probability", "G4" )
KCL_human_downstream<- fread("./KCL/MicroExonator/Control_vs_KCL.diff.downstream_100nt.G4s" )
colnames(KCL_human_downstream) <-c("w.chrom", "w.start", "w.end", "w.strand", "chrom", "start", "end", "strand", "Type", "Psi_A", "Psi_B", "DeltaPsi", "Probability", "G4" )
KCL_human <- merge(KCL_human_upstream[, c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability", "G4") ],
KCL_human_downstream[, c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability", "G4") ],
by=c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability") )
KCL_human[(G4.x>0 | G4.y>0 ), G4_bol:="With G-quadruplex"]
KCL_human[(G4.x==0 & G4.y==0 ), G4_bol:="Without G-quadruplex"]
KCL_human$G4_bol <- factor(KCL_human$G4_bol, levels=c("Without G-quadruplex", "With G-quadruplex") )
KCL_human[end - start > 30, exon:="exon" ]
KCL_human[end - start <= 30, exon:="microexon" ]
size.var=0.5
alpha.var=0.25
ggplot(data=KCL_human[ Type=="CE",]) +
geom_point( aes(x=-DeltaPsi, y=Probability), colour="grey", alpha=alpha.var, size=size.var) +
geom_point(data=KCL_human[Type=="CE" & DeltaPsi>0.1 & Probability>0.9, ], aes(x=-DeltaPsi, y=Probability), colour="skyblue", alpha=alpha.var, size=size.var) +
geom_point(data=KCL_human[Type=="CE" & DeltaPsi<(-0.1) & Probability>0.9, ], aes(x=-DeltaPsi, y=Probability), colour="red", alpha=alpha.var, size=size.var) +
xlim(c(-0.8, 0.8)) +
facet_grid( . ~ G4_bol ) +
xlab("DeltaPSI (Control - KCl)") +
theme_bw()
To highlight NRXN2, SHANK1 and RBM10 we used biomaRt to find the gene name to Ensembl ID correspondence
library(biomaRt)
ensembl = useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl")
KCL_human[ Type=="CE"& DeltaPsi>0.1 & Probability>0.9, ]
chrom start end strand Type DeltaPsi Probability G4.x G4.y G4_bol exon Delta_type
1: chr1 898717 898884 + CE 0.10456 0.983 0 0 Without G-quadruplex exon Skiped
2: chr1 998459 998581 + CE 0.66515 1.000 0 0 Without G-quadruplex exon Skiped
3: chr1 1417925 1417994 + CE 0.19193 1.000 0 0 Without G-quadruplex exon Skiped
4: chr1 1420396 1420551 + CE 0.11443 0.989 0 1 With G-quadruplex exon Skiped
5: chr1 1425072 1425191 + CE 0.25542 0.995 1 0 With G-quadruplex exon Skiped
---
2330: chrX 133372809 133372870 + CE 0.36421 0.968 0 0 Without G-quadruplex exon Skiped
2331: chrX 149882951 149883001 + CE 0.27179 0.976 0 0 Without G-quadruplex exon Skiped
2332: chrX 153224020 153224217 - CE 0.17532 0.999 0 0 Without G-quadruplex exon Skiped
2333: chrX 153585619 153585642 - CE 0.24249 0.999 0 0 Without G-quadruplex microexon Skiped
2334: chrX 153872153 153872305 - CE 0.19742 0.923 1 0 With G-quadruplex exon Skiped
KCL_human[, Coords:=paste(chrom, paste(start, end, sep = "-"), strand, sep=":" )]
whippet.jls.exons.hg19 <- fread("./KCL/whippet.jls.exons.tab")
KCL_human_CE <- merge(KCL_human[Type=="CE", ], whippet.jls.exons.hg19, by.x="Coords", by.y="Potential_Exon")
KCL_human_CE[ , ensembl_gene_id:=vapply(strsplit(KCL_human_CE$Gene, ".", fixed = TRUE), "[", "", 1)]
KCL_human_CE_genes <- data.table(getBM(attributes=c('ensembl_gene_id', "wikigene_description", "hgnc_symbol"),filters = 'ensembl_gene_id', values = unique(vapply(strsplit(KCL_human_CE$Gene, ".", fixed = TRUE), "[", "", 1)) , mart = ensembl))
Batch submitting query [=====>--------------------------------------------------------------------------------------] 7% eta: 2m
Batch submitting query [=========>----------------------------------------------------------------------------------] 10% eta: 11m
Batch submitting query [============>-------------------------------------------------------------------------------] 14% eta: 14m
Batch submitting query [===============>----------------------------------------------------------------------------] 17% eta: 12m
Batch submitting query [==================>-------------------------------------------------------------------------] 21% eta: 10m
Batch submitting query [=====================>----------------------------------------------------------------------] 24% eta: 10m
Batch submitting query [========================>-------------------------------------------------------------------] 28% eta: 14m
Batch submitting query [============================>---------------------------------------------------------------] 31% eta: 15m
Batch submitting query [===============================>------------------------------------------------------------] 34% eta: 15m
Batch submitting query [==================================>---------------------------------------------------------] 38% eta: 14m
Batch submitting query [=====================================>------------------------------------------------------] 41% eta: 13m
Batch submitting query [========================================>---------------------------------------------------] 45% eta: 12m
Batch submitting query [===========================================>------------------------------------------------] 48% eta: 11m
Batch submitting query [===============================================>--------------------------------------------] 52% eta: 10m
Batch submitting query [==================================================>-----------------------------------------] 55% eta: 10m
Batch submitting query [=====================================================>--------------------------------------] 59% eta: 9m
Batch submitting query [========================================================>-----------------------------------] 62% eta: 8m
Batch submitting query [===========================================================>--------------------------------] 66% eta: 7m
Batch submitting query [==============================================================>-----------------------------] 69% eta: 6m
Batch submitting query [==================================================================>-------------------------] 72% eta: 5m
Batch submitting query [=====================================================================>----------------------] 76% eta: 5m
Batch submitting query [========================================================================>-------------------] 79% eta: 4m
Batch submitting query [===========================================================================>----------------] 83% eta: 3m
Batch submitting query [==============================================================================>-------------] 86% eta: 2m
Batch submitting query [=================================================================================>----------] 90% eta: 2m
Batch submitting query [=====================================================================================>------] 93% eta: 1m
Batch submitting query [========================================================================================>---] 97% eta: 38s
Batch submitting query [============================================================================================] 100% eta: 0s
KCL_human_CE <- merge(KCL_human_CE, KCL_human_CE_genes, by="ensembl_gene_id")
KCL_human_CE[ hgnc_symbol=="GRIN1", ][ Type=="CE"& DeltaPsi>0.1 & Probability>0.85, ]
Empty data.table (0 rows and 19 cols): ensembl_gene_id,Coords,chrom,start,end,strand...
KCL_human_CE[ hgnc_symbol=="NRXN2", ][ Type=="CE"& DeltaPsi>0.1 & Probability>0.9, ]
ensembl_gene_id Coords chrom start end strand Type DeltaPsi Probability G4.x G4.y G4_bol
1: ENSG00000110076 chr11:64393935-64394024:- chr11 64393935 64394024 - CE 0.10148 0.976 0 0 Without G-quadruplex
2: ENSG00000110076 chr11:64421168-64421194:- chr11 64421168 64421194 - CE 0.21315 0.992 3 2 With G-quadruplex
exon Delta_type Gene Whippet_Nodes Is_Annotated wikigene_description hgnc_symbol
1: exon Skiped ENSG00000110076.14 41 Y neurexin 2 NRXN2
2: microexon Skiped ENSG00000110076.14 24 Y neurexin 2 NRXN2
KCL_human_CE[ hgnc_symbol=="SHANK1", ][ Type=="CE"& DeltaPsi>0.1 & Probability>0.85, ]
ensembl_gene_id Coords chrom start end strand Type DeltaPsi Probability G4.x G4.y G4_bol exon
1: ENSG00000161681 chr19:51190274-51190297:- chr19 51190274 51190297 - CE 0.18128 0.899 2 2 With G-quadruplex microexon
Delta_type Gene Whippet_Nodes Is_Annotated wikigene_description hgnc_symbol
1: None ENSG00000161681.11 28 Y SH3 and multiple ankyrin repeat domains 1 SHANK1
KCL_human_CE[ hgnc_symbol=="RBM10", ][ Type=="CE"& DeltaPsi>0.1 & Probability>0.9, ]
ensembl_gene_id Coords chrom start end strand Type DeltaPsi Probability G4.x G4.y G4_bol exon
1: ENSG00000182872 chrX:47034418-47034491:+ chrX 47034418 47034491 + CE 0.24869 0.989 1 2 With G-quadruplex exon
Delta_type Gene Whippet_Nodes Is_Annotated wikigene_description hgnc_symbol
1: Skiped ENSG00000182872.11 9 Y RNA binding motif protein 10 RBM10
To analyse all the Whippet node types, we calculate the odd-ratios of being differentially included given the G4 presence or absence
KCL_human[ , diff:="NA"]
KCL_human[ (DeltaPsi<=-0.1 & Probability>=0.9) , diff:="In"]
KCL_human[ (DeltaPsi>0.1 & Probability>=0.9) , diff:="Ex"]
KCL_human_stats <- merge(KCL_human[ G4_bol=="Without G-quadruplex", .(WO_G4=.N) , by=c("Type", "diff") ],
KCL_human[ G4_bol=="With G-quadruplex", .(W_G4=.N) , by=c("Type", "diff") ],
by=c("Type", "diff"))
KCL_human_stats <- merge(KCL_human_stats[diff!="NA"], KCL_human_stats[diff=="NA" , .(Type, WO_G4_NA=WO_G4, W_G4_NA=W_G4) ], by="Type")
KCL_human_stats[, `:=`(WO_G4_fraq=WO_G4/WO_G4_NA, W_G4_fraq=W_G4/W_G4_NA)]
KCL_human_stats[ , OR := W_G4_fraq/WO_G4_fraq]
ggplot(KCL_human_stats) +
geom_tile( aes(Type, diff, fill = log2(OR))) +
scale_fill_gradient2(low="blue", high="red", mid = "grey", midpoint = 0, limits = c(-1.6, 1.6)) +
theme(legend.position = "bottom", legend.direction = "horizontal") +
theme(legend.position = "bottom", legend.direction = "horizontal") + theme(axis.text.x = element_text(angle = 90)) +labs(x = NULL, y = NULL)
We use chi-squared test to calculate the significance
KCL_human_stats
Type diff WO_G4 W_G4 WO_G4_NA W_G4_NA WO_G4_fraq W_G4_fraq OR P_value P_value.Bonferroni
1: AA Ex 181 44 7852 1216 0.023051452 0.036184211 1.5697150 0.0104250635039261 1.459509e-01
2: AA In 149 25 7852 1216 0.018976057 0.020559211 1.0834290 0.798797079630672 1.118316e+01
3: AD Ex 132 41 6161 1590 0.021425093 0.025786164 1.2035496 0.352366558625256 4.933132e+00
4: AD In 117 33 6161 1590 0.018990424 0.020754717 1.0929044 0.730608053514262 1.022851e+01
5: AF Ex 29 10 5305 1562 0.005466541 0.006402049 1.1711334 0.811568365338675 1.136196e+01
6: AF In 21 17 5305 1562 0.003958530 0.010883483 2.7493750 0.00248496072149905 3.478945e-02
7: CE Ex 1932 414 98192 13380 0.019675737 0.030941704 1.5725817 1.26446783231537e-16 1.770255e-15
8: CE In 263 24 98192 13380 0.002678426 0.001793722 0.6696926 0.0718465984186741 1.005852e+00
9: RI Ex 202 62 6858 2078 0.029454652 0.029836381 1.0129599 0.989232440068338 1.384925e+01
10: RI In 135 48 6858 2078 0.019685039 0.023099134 1.1734360 0.39311627657307 5.503628e+00
11: TE Ex 1911 207 59722 7132 0.031998259 0.029024117 0.9070530 0.200964708425952 2.813506e+00
12: TE In 1868 185 59722 7132 0.031278256 0.025939428 0.8293118 0.0180879402239997 2.532312e-01
13: TS Ex 1027 522 36794 19111 0.027912160 0.027314112 0.9785740 0.711119460007881 9.955672e+00
14: TS In 1035 527 36794 19111 0.028129586 0.027575742 0.9803110 0.734230163811721 1.027922e+01
library(plyr)
Fig5.A1 <- ggplot(KCL_human_stats) +
geom_point(aes(Type, diff, size = -log(P_value.Bonferroni), shape=P_value.Bonferroni<0.05, colour=log2(OR) ) ) +
scale_colour_gradient2(low="blue", high="red", mid = "grey", midpoint = 0) +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
Fig5.A1
splice_node_dot_plot <- function(upstream.path, downstream.path ) {
KCL_x_upstream <- fread(upstream.path )
colnames(KCL_x_upstream) <- c("w.chrom", "w.start", "w.end", "w.strand", "chrom", "start", "end", "strand", "Type", "Psi_A", "Psi_B", "DeltaPsi", "Probability", "G4" )
KCL_x_downstream<- fread(downstream.path )
colnames(KCL_x_downstream) <-c("w.chrom", "w.start", "w.end", "w.strand", "chrom", "start", "end", "strand", "Type", "Psi_A", "Psi_B", "DeltaPsi", "Probability", "G4" )
KCL_x <- merge(KCL_x_upstream[, c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability", "G4") ],
KCL_x_downstream[, c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability", "G4") ],
by=c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability") )
#KCL_x <- KCL_x[end-start>30 || Type!="CE", ]
KCL_x[(G4.x>0 | G4.y>0 ), G4_bol:="With G-quadruplex"]
KCL_x[(G4.x==0 & G4.y==0 ), G4_bol:="Without G-quadruplex"]
KCL_x$G4_bol <- factor(KCL_x$G4_bol, levels=c("Without G-quadruplex", "With G-quadruplex") )
KCL_x[ , diff:="NA"]
KCL_x[ (DeltaPsi<=-0.1 & Probability>=0.90) , diff:="In"]
KCL_x[ (DeltaPsi>0.1 & Probability>=0.90) , diff:="Ex"]
KCL_x_stats <- merge(KCL_x[ G4_bol=="Without G-quadruplex", .(WO_G4=.N) , by=c("Type", "diff") ],
KCL_x[ G4_bol=="With G-quadruplex", .(W_G4=.N) , by=c("Type", "diff") ],
by=c("Type", "diff"))
KCL_x_stats <- merge(KCL_x_stats[diff!="NA"], KCL_x_stats[diff=="NA" , .(Type, WO_G4_NA=WO_G4, W_G4_NA=W_G4) ], by="Type")
KCL_x_stats[, `:=`(WO_G4_fraq=WO_G4/WO_G4_NA, W_G4_fraq=W_G4/W_G4_NA)]
KCL_x_stats[ , OR := W_G4_fraq/WO_G4_fraq]
KCL_x_stats.chi <- data.table()
for ( i in unique(KCL_x_stats[Type!="AL"]$Type)){
matrix.ex <- matrix(nrow=2, c(KCL_x_stats[Type==i & diff=="Ex"]$WO_G4_NA, KCL_x_stats[Type==i & diff=="Ex"]$WO_G4, KCL_x_stats[Type==i & diff=="Ex"]$W_G4_NA, KCL_x_stats[Type==i & diff=="Ex"]$W_G4))
matrix.ex_res <- chisq.test(matrix.ex)
matrix.in <- matrix(nrow=2, c(KCL_x_stats[Type==i & diff=="In"]$WO_G4_NA, KCL_x_stats[Type==i & diff=="In"]$WO_G4, KCL_x_stats[Type==i & diff=="In"]$W_G4_NA, KCL_x_stats[Type==i & diff=="In"]$W_G4))
matrix.in_res <- chisq.test(matrix.in)
KCL_x_stats.chi <- rbind(KCL_x_stats.chi, cbind(i, "Ex", matrix.ex_res$p.value))
KCL_x_stats.chi <- rbind(KCL_x_stats.chi, cbind(i, "In", matrix.in_res$p.value))
}
colnames(KCL_x_stats.chi) <- c("Type", "diff", "P_value")
ntest = nrow(KCL_x_stats.chi)
KCL_x_stats.chi[ , `:=`(P_value.Bonferroni=as.numeric(P_value)*ntest) ]
KCL_x_stats <- merge(KCL_x_stats, KCL_x_stats.chi, by=c("Type", "diff"))
ggplot(KCL_x_stats) +
geom_point(aes(Type, diff, size = -log(P_value.Bonferroni), shape=P_value.Bonferroni<0.05, colour=log2(OR) ) ) +
scale_colour_gradient2(low="blue", high="red", mid = "grey", midpoint = 0) +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
return(KCL_x_stats)
}
upstream.path = "./KCL/MicroExonator/ESC-derived_neuron_CD1.diff.upstream_100nt.G4s"
downstream.path = "./KCL/MicroExonator/ESC-derived_neuron_CD1.diff.downstream_100nt.G4s"
splice_node_dot_plot2 <- function(upstream.path, downstream.path ) {
KCL_x_upstream <- fread(upstream.path )
colnames(KCL_x_upstream) <- c("w.chrom", "w.start", "w.end", "w.strand", "chrom", "start", "end", "strand", "Type", "Psi_A", "Psi_B", "DeltaPsi", "Probability", "G4" )
KCL_x_downstream<- fread(downstream.path )
colnames(KCL_x_downstream) <-c("w.chrom", "w.start", "w.end", "w.strand", "chrom", "start", "end", "strand", "Type", "Psi_A", "Psi_B", "DeltaPsi", "Probability", "G4" )
KCL_x <- merge(KCL_x_upstream[, c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability", "G4") ],
KCL_x_downstream[, c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability", "G4") ],
by=c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability") )
#KCL_x <- KCL_x[end-start>30 || Type!="CE", ]
KCL_x[(G4.x>0 | G4.y>0 ), G4_bol:="With G-quadruplex"]
KCL_x[(G4.x==0 & G4.y==0 ), G4_bol:="Without G-quadruplex"]
KCL_x$G4_bol <- factor(KCL_x$G4_bol, levels=c("Without G-quadruplex", "With G-quadruplex") )
KCL_x[ , diff:="NA"]
KCL_x[ (DeltaPsi<=-0.1 & Probability>=0.90) , diff:="In"]
KCL_x[ (DeltaPsi>0.1 & Probability>=0.90) , diff:="Ex"]
KCL_x_stats <- merge(KCL_x[ G4_bol=="Without G-quadruplex", .(WO_G4=.N) , by=c("Type", "diff") ],
KCL_x[ G4_bol=="With G-quadruplex", .(W_G4=.N) , by=c("Type", "diff") ],
by=c("Type", "diff"))
KCL_x_stats <- merge(KCL_x_stats[diff!="NA"], KCL_x_stats[diff=="NA" , .(Type, WO_G4_NA=WO_G4, W_G4_NA=W_G4) ], by="Type")
KCL_x_stats[, `:=`(WO_G4_fraq=WO_G4/WO_G4_NA, W_G4_fraq=W_G4/W_G4_NA)]
KCL_x_stats[ , OR := W_G4_fraq/WO_G4_fraq]
KCL_x_stats.chi <- data.table()
for ( i in unique(KCL_x_stats[Type!="AL"]$Type)){
matrix <- matrix(nrow=2, c(KCL_x_stats[Type==i & diff=="In"]$WO_G4, KCL_x_stats[Type==i & diff=="Ex"]$WO_G4, KCL_x_stats[Type==i & diff=="In"]$W_G4, KCL_x_stats[Type==i & diff=="Ex"]$W_G4))
matrix.res <- chisq.test(matrix)
KCL_x_stats.chi <- rbind(KCL_x_stats.chi, cbind(i, matrix.res$p.value))
}
colnames(KCL_x_stats.chi) <- c("Type", "P_value")
ntest = nrow(KCL_x_stats.chi)
KCL_x_stats.chi[ , `:=`(P_value.Bonferroni=as.numeric(P_value)*ntest) ]
#KCL_x_stats <- merge(KCL_x_stats, KCL_x_stats.chi, by=c("Type", "diff"))
#ggplot(KCL_x_stats.chi) +
# geom_point(aes(Type, diff, size = -log(P_value.Bonferroni), shape=P_value.Bonferroni<0.05, colour=log2(OR) ) ) +
# scale_colour_gradient2(low="blue", high="red", mid = "grey", midpoint = 0) +
# theme_bw() +
# theme(legend.position = "top", legend.direction = "horizontal")
return(KCL_x_stats.chi)
}
diff_G4_ME_table <- function(upstream.path, downstream.path, dist_lim ) {
KCL_x_upstream <- fread(upstream.path )
colnames(KCL_x_upstream) <- c("w.chrom", "w.start", "w.end", "w.strand", "chrom", "start", "end", "strand", "Type", "Psi_A", "Psi_B", "DeltaPsi", "Probability", "gchrom", "gstart", "gend", "gscore", "exon_dist" )
KCL_x_upstream[ ,dist:=((gstart + (gend- gstart)/2) -w.start ) ]
#KCL_x[(dist.x<=dist_lim | dist.y<=dist_lim ), G4_bol:="With G-quadruplex"]
KCL_x_downstream<- fread(downstream.path )
colnames(KCL_x_downstream) <- c("w.chrom", "w.start", "w.end", "w.strand", "chrom", "start", "end", "strand", "Type", "Psi_A", "Psi_B", "DeltaPsi", "Probability", "gchrom", "gstart", "gend", "gscore", "exon_dist" )
KCL_x_downstream[ ,dist:=((gstart + (gend- gstart)/2)) - w.start ]
KCL_x <- merge(KCL_x_upstream[, c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability", "dist") ],
KCL_x_downstream[, c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability", "dist") ],
by=c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability") )
#KCL_x <- KCL_x[end-start>30 || Type!="CE", ]
KCL_x[ , G4_bol:="Without G-quadruplex"]
KCL_x[strand=="+" & ((dist.x >= -dist_lim & dist.x <= 0) | ( dist.y >=0 & dist.y<=dist_lim)) , G4_bol:="With G-quadruplex"]
KCL_x[strand=="-" & ((dist.y >= -dist_lim & dist.y <= 0) | ( dist.x >=0 & dist.x<=dist_lim)) , G4_bol:="With G-quadruplex"]
KCL_x$G4_bol <- factor(KCL_x$G4_bol, levels=c("Without G-quadruplex", "With G-quadruplex") )
KCL_x[ , diff:="NA"]
KCL_x[ (DeltaPsi<=-0.1 & Probability>=0.90) , diff:="In"]
KCL_x[ (DeltaPsi>0.1 & Probability>=0.90) , diff:="Ex"]
KCL_x <- KCL_x[Type=="CE"]
KCL_x[ , exon_class:="exon"]
KCL_x[end-start<=30, exon_class:="microexon" ]
return(KCL_x)
}
upstream.path = "./Exons_G4s/human.exons.tvs.upstream.G4seq_K"
downstream.path = "./Exons_G4s/human.exons.tvs.downstream.G4seq_K"
G4_ME_table <- function(upstream.path, downstream.path, dist_lim ) {
KCL_x_upstream <- fread(upstream.path )
colnames(KCL_x_upstream) <- c( "chrom", "sstart", "send", "sstrand", "start", "end", "strand", "gchrom", "gstart", "gend", "gscore", "exon_dist" )
KCL_x_upstream[ ,dist:=(sstart - (gstart + (gend- gstart)/2)) ]
#KCL_x[(dist.x<=dist_lim | dist.y<=dist_lim ), G4_bol:="With G-quadruplex"]
KCL_x_downstream<- fread(downstream.path )
colnames(KCL_x_downstream) <- c( "chrom", "sstart", "send", "strand", "start", "end", "strand", "gchrom", "gstart", "gend", "gscore", "exon_dist" )
KCL_x_downstream[ ,dist:=(sstart - (gstart + (gend- gstart)/2)) ]
KCL_x <- merge(KCL_x_upstream[, c( "chrom", "start", "end", "strand", "dist") ],
KCL_x_downstream[, c( "chrom", "start", "end", "strand", "dist") ],
by=c( "chrom", "start", "end", "strand") )
#KCL_x <- KCL_x[end-start>30 || Type!="CE", ]
KCL_x[ , G4_bol:="Without G-quadruplex"]
KCL_x[ strand=="+" & ((dist.x >= -dist_lim & dist.x <= 0) | ( dist.y >=0 & dist.y<=dist_lim)) , G4_bol:="With G-quadruplex"]
KCL_x[ strand=="-" & ((dist.y >= -dist_lim & dist.y <= 0) | ( dist.x >=0 & dist.x<=dist_lim)) , G4_bol:="With G-quadruplex"]
KCL_x$G4_bol <- factor(KCL_x$G4_bol, levels=c("Without G-quadruplex", "With G-quadruplex") )
KCL_x[ , exon_class:="exon"]
KCL_x[end-start<=30, exon_class:="microexon" ]
return(KCL_x)
}
KCL_human_CE <- KCL_human[ , paste(chrom, start, end, sep="_" ) ]
human.exons.upstream.G4s <- fread("./Exons_G4s/human.exons.tvs.upstream.G4s")
human.exons.downstream.G4s <- fread("./Exons_G4s/human.exons.tvs.downstream.G4s")
colnames(human.exons.upstream.G4s) <- c( "chrom", "sstart", "send", "sstrand", "start", "end", "strand", "gchrom", "gstart", "gend", "gscore", "exon_dist" )
human.exons.upstream.G4s[ ,dist:=(sstart - (gstart + (gend- gstart)/2)) ]
human.exons.upstream.G4s[, exon_len:=end-start]
human.exons.upstream.G4s[ , G4_bol:="Without G-quadruplex"]
human.exons.upstream.G4s[ dist>=-100 & dist<=0 , G4_bol:="With G-quadruplex"]
human.exons.upstream.G4s[ , ID:=paste(chrom, start, end, sep="_" )]
human.exons.upstream.G4s[, filter:="Out"]
human.exons.upstream.G4s[ ID %in% KCL_human_CE, ]
chrom sstart send sstrand start end strand gchrom gstart gend gscore exon_dist dist exon_len
1: chr1 15038 15039 - 15005 15038 - chr1 16797 16846 16797_16846 1759 -1783.5 33
2: chr1 15947 15948 - 15904 15947 - chr1 16797 16846 16797_16846 850 -874.5 43
3: chr1 16745 16746 - 16607 16745 - chr1 16797 16846 16797_16846 52 -76.5 138
4: chr1 17364 17365 - 17233 17364 - chr1 17545 17594 17545_17594 181 -205.5 131
5: chr1 17504 17505 - 17498 17504 - chr1 17545 17594 17545_17594 41 -65.5 6
---
human.exons.downstream.G4s <- fread("./Exons_G4s/human.exons.tvs.downstream.G4seq_PDS")
colnames(human.exons.downstream.G4s) <- c( "chrom", "sstart", "send", "sstrand", "start", "end", "strand", "gchrom", "gstart", "gend", "gscore", "exon_dist" )
human.exons.downstream.G4s[ ,dist:=( (gstart + (gend- gstart)/2) - sstart) ]
human.exons.downstream.G4s[ sstrand=="-", dist:=( sstart - (gstart + (gend- gstart)/2)) ]
human.exons.downstream.G4s[, exon_len:=end-start]
human.exons.downstream.G4s[ , G4_bol:="Without G-quadruplex"]
human.exons.downstream.G4s[ dist<=100 & dist>=0 , G4_bol:="With G-quadruplex"]
human.exons.downstream.G4s[, exon_class:="exon"]
human.exons.downstream.G4s[ exon_len<=30, exon_class:="microexon"]
human.exons.downstream.G4s.2x2 <- matrix(ncol = 2,
c(nrow(human.exons.downstream.G4s[ exon_class=="exon" & G4_bol=="Without G-quadruplex"]),
nrow(human.exons.downstream.G4s[ exon_class=="exon" & G4_bol=="With G-quadruplex"]),
nrow(human.exons.downstream.G4s[ exon_class=="microexon" & G4_bol=="Without G-quadruplex"]),
nrow(human.exons.downstream.G4s[ exon_class=="microexon" & G4_bol=="With G-quadruplex"]) ))
chisq.test(human.exons.downstream.G4s.2x2)
Pearson's Chi-squared test with Yates' continuity correction
data: human.exons.downstream.G4s.2x2
X-squared = 8.2286, df = 1, p-value = 0.004123
hg19_ME_table_G4s[, median(exon_len), by=G4_bol]
G4_bol V1
1: Without G-quadruplex 147
2: With G-quadruplex 155
matrix(ncol=2, c( ))
human.ME_g4.stats <- data.table()
hg19_ME_table_G4s <- G4_ME_table("./Exons_G4s/human.exons.tvs.upstream.G4s" , "./Exons_G4s/human.exons.tvs.downstream.G4s", 100 )
hg19_ME_table_G4s.2x2 <- matrix(ncol = 2,
c(nrow(hg19_ME_table_G4s[ exon_class=="exon" & G4_bol=="Without G-quadruplex"]),
nrow(hg19_ME_table_G4s[ exon_class=="exon" & G4_bol=="With G-quadruplex"]),
nrow(hg19_ME_table_G4s[ exon_class=="microexon" & G4_bol=="Without G-quadruplex"]),
nrow(hg19_ME_table_G4s[ exon_class=="microexon" & G4_bol=="With G-quadruplex"]) ))
hg19_ME_table_G4s[ , exon_len:=end-start]
colnames(hg19_ME_table_G4s.2x2) <- c("exon", "microexon")
rownames(hg19_ME_table_G4s.2x2) <- c("Without G-quadruplex", "With G-quadruplex")
human.ME_g4.stats <- rbind(human.ME_g4.stats,
cbind(
"motif",
chisq.test( hg19_ME_table_G4s.2x2)$p.value,
(hg19_ME_table_G4s.2x2[ 2 , 2 ]/hg19_ME_table_G4s.2x2[ 1 , 2 ]) / (hg19_ME_table_G4s.2x2[ 2 , 1 ]/hg19_ME_table_G4s.2x2[ 1 , 1 ])
))
hg19_ME_table_K <- G4_ME_table("./Exons_G4s/human.exons.tvs.upstream.G4seq_K" , "./Exons_G4s/human.exons.tvs.downstream.G4seq_K", 100 )
hg19_ME_table_K.2x2 <- matrix(ncol = 2,
c(nrow(hg19_ME_table_K[ exon_class=="exon" & G4_bol=="Without G-quadruplex"]),
nrow(hg19_ME_table_K[ exon_class=="exon" & G4_bol=="With G-quadruplex"]),
nrow(hg19_ME_table_K[ exon_class=="microexon" & G4_bol=="Without G-quadruplex"]),
nrow(hg19_ME_table_K[ exon_class=="microexon" & G4_bol=="With G-quadruplex"]) ))
chisq.test( hg19_ME_table_K.2x2)
Pearson's Chi-squared test with Yates' continuity correction
data: hg19_ME_table_K.2x2
X-squared = 775.72, df = 1, p-value < 2.2e-16
human.ME_g4.stats <- rbind(human.ME_g4.stats,
cbind(
"K+",
chisq.test( hg19_ME_table_K.2x2)$p.value,
(hg19_ME_table_K.2x2[ 2 , 2 ]/hg19_ME_table_K.2x2[ 1 , 2 ]) / (hg19_ME_table_K.2x2[ 2 , 1 ]/hg19_ME_table_K.2x2[ 1 , 1 ])
))
hg19_ME_table_PDS <- G4_ME_table("./Exons_G4s/human.exons.tvs.upstream.G4seq_PDS" , "./Exons_G4s/human.exons.tvs.downstream.G4seq_PDS", 100 )
hg19_ME_table_PDS.2x2 <- matrix(ncol = 2,
c(nrow(hg19_ME_table_PDS[ exon_class=="exon" & G4_bol=="Without G-quadruplex"]),
nrow(hg19_ME_table_PDS[ exon_class=="exon" & G4_bol=="With G-quadruplex"]),
nrow(hg19_ME_table_PDS[ exon_class=="microexon" & G4_bol=="Without G-quadruplex"]),
nrow(hg19_ME_table_PDS[ exon_class=="microexon" & G4_bol=="With G-quadruplex"]) ))
chisq.test( hg19_ME_table_PDS.2x2)
Pearson's Chi-squared test with Yates' continuity correction
data: hg19_ME_table_PDS.2x2
X-squared = 1311.3, df = 1, p-value < 2.2e-16
human.ME_g4.stats <- rbind(human.ME_g4.stats,
cbind(
"PDS",
chisq.test( hg19_ME_table_PDS.2x2)$p.value,
(hg19_ME_table_PDS.2x2[ 2 , 2 ]/hg19_ME_table_PDS.2x2[ 1 , 2 ]) / (hg19_ME_table_PDS.2x2[ 2 , 1 ]/hg19_ME_table_PDS.2x2[ 1 , 1 ])
))
human.ME_g4.stats
V1 V2 V3
1: motif 5.27431665031594e-46 1.43471802302067
2: K+ 1.62313466930488e-21 1.31759263167337
3: PDS 1.90542366661142e-47 1.3092934132111
primary_cortical_neuron_DIV4_CD1_K_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV4_CD1.diff.upstream.G4seq_K" , "./KCL/MicroExonator/closest/primary_cortical_neuron_DIV4_CD1.diff.downstream.G4seq_K", 100 )
ESC_derived_neuron_CD1_K_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/ESC-derived_neuron_CD1.diff.upstream.G4seq_K" , "./KCL/MicroExonator/closest/ESC-derived_neuron_CD1.diff.downstream.G4seq_K", 100 )
primary_cortical_neuron_DIV10_CD1_K_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_CD1.diff.upstream.G4seq_K" , "./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_CD1.diff.downstream.G4seq_K", 100 )
primary_cortical_neuron_DIV10_Tc1_K_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_Tc1.diff.upstream.G4seq_K" , "./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_Tc1.diff.downstream.G4seq_K", 100 )
total_mouse_K_ME_table <- unique(rbind(primary_cortical_neuron_DIV4_CD1_K_ME_table[ , c("chrom" ,"start", "end", "strand", "Type", "G4_bol", "exon_class")],
ESC_derived_neuron_CD1_K_ME_table[ , c("chrom" ,"start", "end", "strand", "Type", "G4_bol", "exon_class")],
primary_cortical_neuron_DIV10_CD1_K_ME_table[ , c("chrom" ,"start", "end", "strand", "Type", "G4_bol", "exon_class")],
primary_cortical_neuron_DIV10_Tc1_K_ME_table[ , c("chrom" ,"start", "end", "strand", "Type", "G4_bol", "exon_class")]))
total_mouse_K_ME_table.2x2 <- matrix(ncol = 2,
c(nrow(total_mouse_K_ME_table[ exon_class=="exon" & G4_bol=="Without G-quadruplex"]),
nrow(total_mouse_K_ME_table[ exon_class=="exon" & G4_bol=="With G-quadruplex"]),
nrow(total_mouse_K_ME_table[ exon_class=="microexon" & G4_bol=="Without G-quadruplex"]),
nrow(total_mouse_K_ME_table[ exon_class=="microexon" & G4_bol=="With G-quadruplex"]) ))
chisq.test( total_mouse_K_ME_table.2x2)
Pearson's Chi-squared test with Yates' continuity correction
data: total_mouse_K_ME_table.2x2
X-squared = 1.9867, df = 1, p-value = 0.1587
colnames(total_mouse_K_ME_table.2x2) <- c("exon", "microexon")
rownames(total_mouse_K_ME_table.2x2) <- c("Without G-quadruplex", "With G-quadruplex")
primary_cortical_neuron_DIV4_CD1_PDS_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV4_CD1.diff.upstream.G4seq_PDS" , "./KCL/MicroExonator/closest/primary_cortical_neuron_DIV4_CD1.diff.downstream.G4seq_PDS", 100 )
ESC_derived_neuron_CD1_PDS_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/ESC-derived_neuron_CD1.diff.upstream.G4seq_PDS" , "./KCL/MicroExonator/closest/ESC-derived_neuron_CD1.diff.downstream.G4seq_PDS", 100 )
primary_cortical_neuron_DIV10_CD1_PDS_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_CD1.diff.upstream.G4seq_PDS" , "./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_CD1.diff.downstream.G4seq_PDS", 100 )
primary_cortical_neuron_DIV10_Tc1_PDS_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_Tc1.diff.upstream.G4seq_PDS" , "./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_Tc1.diff.downstream.G4seq_PDS", 100 )
total_mouse_PDS_ME_table <- unique(rbind(primary_cortical_neuron_DIV4_CD1_PDS_ME_table[ , c("chrom" ,"start", "end", "strand", "Type", "G4_bol", "exon_class")],
ESC_derived_neuron_CD1_PDS_ME_table[ , c("chrom" ,"start", "end", "strand", "Type", "G4_bol", "exon_class")],
primary_cortical_neuron_DIV10_CD1_PDS_ME_table[ , c("chrom" ,"start", "end", "strand", "Type", "G4_bol", "exon_class")],
primary_cortical_neuron_DIV10_Tc1_PDS_ME_table[ , c("chrom" ,"start", "end", "strand", "Type", "G4_bol", "exon_class")]))
total_mouse_PDS_ME_table.2x2 <- matrix(ncol = 2,
c(nrow(total_mouse_PDS_ME_table[ exon_class=="exon" & G4_bol=="Without G-quadruplex"]),
nrow(total_mouse_PDS_ME_table[ exon_class=="exon" & G4_bol=="With G-quadruplex"]),
nrow(total_mouse_PDS_ME_table[ exon_class=="microexon" & G4_bol=="Without G-quadruplex"]),
nrow(total_mouse_PDS_ME_table[ exon_class=="microexon" & G4_bol=="With G-quadruplex"]) ))
chisq.test( total_mouse_PDS_ME_table.2x2)
Pearson's Chi-squared test with Yates' continuity correction
data: total_mouse_PDS_ME_table.2x2
X-squared = 3.915e-27, df = 1, p-value = 1
human_motif_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/Control_vs_KCL.diff.upstream.G4s" , "./KCL/MicroExonator/closest/Control_vs_KCL.diff.downstream.G4s", 100 )
|--------------------------------------------------|
|==================================================|
human_K_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/Control_vs_KCL.diff.upstream.G4seq_K" , "./KCL/MicroExonator/closest/Control_vs_KCL.diff.downstream.G4seq_K", 100 )
human_PDS_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/Control_vs_KCL.diff.upstream.G4seq_PDS" , "./KCL/MicroExonator/closest/Control_vs_KCL.diff.downstream.G4seq_PDS", 100 )
human_motif_ME_table[, ID:=paste( chrom, strand, start, end , sep="_")]
human_K_ME_table[, ID:=paste( chrom, strand, start, end , sep="_")]
human_PDS_ME_table[, ID:=paste( chrom, strand, start, end , sep="_")]
All_human<- data.table(unique(c(
human_motif_ME_table[G4_bol=="With G-quadruplex", ID],
human_K_ME_table[G4_bol=="With G-quadruplex", ID],
human_PDS_ME_table[G4_bol=="With G-quadruplex", ID])))
colnames(All_human) <- "ID"
All_human[ ID %in% human_motif_ME_table[abs(DeltaPsi)>=0.1 & Probability>=0.9 & G4_bol=="With G-quadruplex", ID ], diff_motif:=TRUE ]
All_human[ ID %in% human_K_ME_table[abs(DeltaPsi)>=0.1 & Probability>=0.9 & G4_bol=="With G-quadruplex", ID ], diff_K:=TRUE ]
All_human[ ID %in% human_PDS_ME_table[abs(DeltaPsi)>=0.1 & Probability>=0.9 & G4_bol=="With G-quadruplex", ID ], diff_:=TRUE ]
All_human <- cbind(All_human, rowSums(is.na(All_human)))
View(All_human.mouse.diff.gene[order(V2.y, V2.x )][, c("ID", "mID", "V2.x", "V2.y", "wikigene_description", "hgnc_symbol")] )
Error in View : object 'V2.y' not found
KCL_human[ID=""]
total_mouse_PDS_ME_table[G4_bol=="Without G-quadruplex", mean(exon_len) ]
[1] 135.2497
primary_cortical_neuron_DIV4_CD1_K_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV4_CD1.diff.upstream.G4seq_K" , "./KCL/MicroExonator/closest/primary_cortical_neuron_DIV4_CD1.diff.downstream.G4seq_K", 100 )
primary_cortical_neuron_DIV4_CD1_K_ME_table.2x2 <- matrix(ncol = 2,
c(nrow(primary_cortical_neuron_DIV4_CD1_K_ME_table[ exon_class=="exon" & G4_bol=="Without G-quadruplex"]),
nrow(primary_cortical_neuron_DIV4_CD1_K_ME_table[ exon_class=="exon" & G4_bol=="With G-quadruplex"]),
nrow(primary_cortical_neuron_DIV4_CD1_K_ME_table[ exon_class=="microexon" & G4_bol=="Without G-quadruplex"]),
nrow(primary_cortical_neuron_DIV4_CD1_K_ME_table[ exon_class=="microexon" & G4_bol=="With G-quadruplex"]) ))
chisq.test( primary_cortical_neuron_DIV4_CD1_K_ME_table.2x2)
Pearson's Chi-squared test with Yates' continuity correction
data: primary_cortical_neuron_DIV4_CD1_K_ME_table.2x2
X-squared = 2.0509, df = 1, p-value = 0.1521
primary_cortical_neuron_DIV4_CD1_PDS_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV4_CD1.diff.upstream.G4seq_PDS" , "./KCL/MicroExonator/closest/primary_cortical_neuron_DIV4_CD1.diff.downstream.G4seq_PDS", 100 )
primary_cortical_neuron_DIV4_CD1_PDS_ME_table.2x2 <- matrix(ncol = 2,
c(nrow(primary_cortical_neuron_DIV4_CD1_PDS_ME_table[ exon_class=="exon" & G4_bol=="Without G-quadruplex"]),
nrow(primary_cortical_neuron_DIV4_CD1_PDS_ME_table[ exon_class=="exon" & G4_bol=="With G-quadruplex"]),
nrow(primary_cortical_neuron_DIV4_CD1_PDS_ME_table[ exon_class=="microexon" & G4_bol=="Without G-quadruplex"]),
nrow(primary_cortical_neuron_DIV4_CD1_PDS_ME_table[ exon_class=="microexon" & G4_bol=="With G-quadruplex"]) ))
chisq.test( primary_cortical_neuron_DIV4_CD1_PDS_ME_table.2x2)
Pearson's Chi-squared test with Yates' continuity correction
data: primary_cortical_neuron_DIV4_CD1_PDS_ME_table.2x2
X-squared = 1.0594, df = 1, p-value = 0.3034
Control_vs_KCL_K_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/Control_vs_KCL.diff.upstream.G4seq_K" , "./KCL/MicroExonator/closest/Control_vs_KCL.diff.downstream.G4seq_K", 100 )
Control_vs_KCL_K_ME_table.2x2 <- matrix(ncol = 2,
c(nrow(Control_vs_KCL_K_ME_table[ exon_class=="exon" & G4_bol=="Without G-quadruplex"]),
nrow(Control_vs_KCL_K_ME_table[ exon_class=="exon" & G4_bol=="With G-quadruplex"]),
nrow(Control_vs_KCL_K_ME_table[ exon_class=="microexon" & G4_bol=="Without G-quadruplex"]),
nrow(Control_vs_KCL_K_ME_table[ exon_class=="microexon" & G4_bol=="With G-quadruplex"]) ))
chisq.test( Control_vs_KCL_K_ME_table.2x2)
Pearson's Chi-squared test with Yates' continuity correction
data: Control_vs_KCL_K_ME_table.2x2
X-squared = 0.026068, df = 1, p-value = 0.8717
Control_vs_KCL_PDS_ME_table <- diff_G4_ME_table("./KCL/MicroExonator/closest/Control_vs_KCL.diff.upstream.G4seq_PDS" , "./KCL/MicroExonator/closest/Control_vs_KCL.diff.downstream.G4seq_K", 100 )
Control_vs_KCL_PDS_ME_table.2x2 <- matrix(ncol = 2,
c(nrow(Control_vs_KCL_PDS_ME_table[ exon_class=="exon" & G4_bol=="Without G-quadruplex"]),
nrow(Control_vs_KCL_PDS_ME_table[ exon_class=="exon" & G4_bol=="With G-quadruplex"]),
nrow(Control_vs_KCL_PDS_ME_table[ exon_class=="microexon" & G4_bol=="Without G-quadruplex"]),
nrow(Control_vs_KCL_PDS_ME_table[ exon_class=="microexon" & G4_bol=="With G-quadruplex"]) ))
chisq.test( Control_vs_KCL_PDS_ME_table.2x2)
Pearson's Chi-squared test with Yates' continuity correction
data: Control_vs_KCL_PDS_ME_table.2x2
X-squared = 10.324, df = 1, p-value = 0.001313
#upstream.path = "./KCL/MicroExonator/closest/primary_cortical_neuron_DIV4_CD1.diff.upstream.G4seq_K"
#downstream.path = "./KCL/MicroExonator/closest/primary_cortical_neuron_DIV4_CD1.diff.downstream.G4seq_K"
#dist_lim = 150
upstream.path = "./AQ1/Control_vs_1mu.diff.downstream.G4seq_K"
downstream.path = "./AQ1/Control_vs_1mu.diff.upstream.G4seq_K"
dist_lim = 100
splice_node_dot_plot3 <- function(upstream.path, downstream.path, dist_lim ) {
KCL_x_upstream <- fread(upstream.path )
colnames(KCL_x_upstream) <- c("w.chrom", "w.start", "w.end", "w.strand", "chrom", "start", "end", "strand", "Type", "Psi_A", "Psi_B", "DeltaPsi", "Probability", "gchrom", "gstart", "gend", "gscore", "exon_dist" )
KCL_x_upstream[ ,dist:=abs(w.start - (gstart + (gend- gstart)/2)) ]
KCL_x_downstream<- fread(downstream.path )
colnames(KCL_x_downstream) <- c("w.chrom", "w.start", "w.end", "w.strand", "chrom", "start", "end", "strand", "Type", "Psi_A", "Psi_B", "DeltaPsi", "Probability", "gchrom", "gstart", "gend", "gscore", "exon_dist" )
KCL_x_downstream[ ,dist:=abs(w.start - (gstart + (gend- gstart)/2)) ]
KCL_x <- merge(KCL_x_upstream[, c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability", "dist") ],
KCL_x_downstream[, c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability", "dist") ],
by=c("chrom", "start", "end", "strand", "Type" , "DeltaPsi", "Probability") )
#KCL_x <- KCL_x[end-start>30 || Type!="CE", ]
KCL_x[(dist.x<=dist_lim | dist.y<=dist_lim ), G4_bol:="With G-quadruplex"]
KCL_x[(dist.x>dist_lim & dist.y>dist_lim ), G4_bol:="Without G-quadruplex"]
KCL_x$G4_bol <- factor(KCL_x$G4_bol, levels=c("Without G-quadruplex", "With G-quadruplex") )
KCL_x[ , diff:="NA"]
KCL_x[ (DeltaPsi<=-0.1 & Probability>=0.90) , diff:="In"]
KCL_x[ (DeltaPsi>0.1 & Probability>=0.90) , diff:="Ex"]
KCL_x_stats <- merge(KCL_x[ G4_bol=="Without G-quadruplex", .(WO_G4=.N) , by=c("Type", "diff") ],
KCL_x[ G4_bol=="With G-quadruplex", .(W_G4=.N) , by=c("Type", "diff") ],
by=c("Type", "diff"))
KCL_x_stats <- merge(KCL_x_stats[diff!="NA"], KCL_x_stats[diff=="NA" , .(Type, WO_G4_NA=WO_G4, W_G4_NA=W_G4) ], by="Type")
KCL_x_stats[, `:=`(WO_G4_fraq=WO_G4/WO_G4_NA, W_G4_fraq=W_G4/W_G4_NA)]
KCL_x_stats[ , OR := W_G4_fraq/WO_G4_fraq]
KCL_x_stats.chi <- data.table()
for ( i in unique(KCL_x_stats[Type!="AL" & Type!="AF"]$Type)){
matrix.ex <- matrix(nrow=2, c(KCL_x_stats[Type==i & diff=="Ex"]$WO_G4_NA, KCL_x_stats[Type==i & diff=="Ex"]$WO_G4, KCL_x_stats[Type==i & diff=="Ex"]$W_G4_NA, KCL_x_stats[Type==i & diff=="Ex"]$W_G4))
matrix.ex_res <- chisq.test(matrix.ex, correct=TRUE)
matrix.in <- matrix(nrow=2, c(KCL_x_stats[Type==i & diff=="In"]$WO_G4_NA, KCL_x_stats[Type==i & diff=="In"]$WO_G4, KCL_x_stats[Type==i & diff=="In"]$W_G4_NA, KCL_x_stats[Type==i & diff=="In"]$W_G4))
matrix.in_res <- chisq.test(matrix.in, correct=TRUE)
KCL_x_stats.chi <- rbind(KCL_x_stats.chi, cbind(i, "Ex", matrix.ex_res$p.value))
KCL_x_stats.chi <- rbind(KCL_x_stats.chi, cbind(i, "In", matrix.in_res$p.value))
}
colnames(KCL_x_stats.chi) <- c("Type", "diff", "P_value")
ntest = nrow(KCL_x_stats.chi)
KCL_x_stats.chi[ , `:=`(P_value.Bonferroni=as.numeric(P_value)*ntest) ]
KCL_x_stats <- merge(KCL_x_stats, KCL_x_stats.chi, by=c("Type", "diff"))
ggplot(KCL_x_stats) +
geom_point(aes(Type, diff, size = -log(P_value.Bonferroni), shape=P_value.Bonferroni<0.05, colour=log2(OR) ) ) +
scale_colour_gradient2(low="blue", high="red", mid = "grey", midpoint = 0) +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
return(KCL_x_stats)
}
test
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14
1: chr10 33247060 33247260 - chr10 33247156 33247160 - TS 0.20852000 0.29307000 -0.08455300 0.681 2
2: chr10 33247055 33247255 - chr10 33247148 33247155 - TS 0.00632510 0.00397540 0.00234980 0.614 2
3: chr10 33247047 33247247 - chr10 33247147 33247147 - TS 0.00643090 0.00417170 0.00225920 0.593 2
4: chr10 33247046 33247246 - chr10 33247138 33247146 - TS 0.20339000 0.22663000 -0.02324300 0.626 2
5: chr10 33247037 33247237 - chr10 33247125 33247137 - TS 0.00637130 0.02837200 -0.02200100 0.709 2
---
280986: chrY 2606141 2606341 + chrY 2606241 2606297 + CE 0.99405000 0.99588000 -0.00183480 0.565 0
280987: chrY 2608720 2608920 + chrY 2608820 2609142 + TE 0.00066347 0.00049058 0.00017289 0.564 0
280988: chrY 2609043 2609243 + chrY 2609143 2609166 + TE 0.46610000 0.45772000 0.00837880 0.558 0
280989: chrY 2609067 2609267 + chrY 2609167 2609350 + TE 0.53409000 0.54219000 -0.00810420 0.553 0
280990: chrY 7171878 7172078 + chrY 7171978 7172146 + CE 0.89609000 0.92204000 -0.02594900 0.564 0
AQ1.1.PDS
Type diff WO_G4 W_G4 WO_G4_NA W_G4_NA WO_G4_fraq W_G4_fraq OR P_value P_value.Bonferroni
1: AA Ex 100 33 3417 2090 0.029265438 0.015789474 0.5395263 0.00269924680585348 3.239096e-02
2: AA In 100 60 3417 2090 0.029265438 0.028708134 0.9809569 0.973326078843511 1.167991e+01
3: AD Ex 74 40 2384 1659 0.031040268 0.024110910 0.7767623 0.23918041819642 2.870165e+00
4: AD In 99 58 2384 1659 0.041526846 0.034960820 0.8418848 0.347044570353516 4.164535e+00
5: CE Ex 978 182 35437 17223 0.027598273 0.010567265 0.3828959 2.32034593344643e-34 2.784415e-33
6: CE In 277 94 35437 17223 0.007816689 0.005457818 0.6982263 0.00307047698059758 3.684572e-02
7: RI Ex 41 66 2608 2897 0.015720859 0.022782188 1.4491695 0.0782381828984119 9.388582e-01
8: RI In 188 168 2608 2897 0.072085890 0.057991025 0.8044712 0.0530363771218024 6.364365e-01
9: TE Ex 1016 325 38550 13647 0.026355383 0.023814758 0.9036013 0.123388611952283 1.480663e+00
10: TE In 1185 373 38550 13647 0.030739300 0.027332014 0.8891554 0.054440043888416 6.532805e-01
11: TS Ex 358 290 15188 15858 0.023571240 0.018287300 0.7758310 0.00164147635842411 1.969772e-02
12: TS In 388 390 15188 15858 0.025546484 0.024593265 0.9626869 0.625880320055632 7.510564e+00
HEK.PDS.motif
Type diff WO_G4 W_G4 WO_G4_NA W_G4_NA WO_G4_fraq W_G4_fraq OR P_value P_value.Bonferroni
1: AA Ex 24 1 8692 1106 0.002761160 0.0009041591 0.3274563 0.404133875658452 4.8496065
2: AA In 33 6 8692 1106 0.003796595 0.0054249548 1.4289002 0.58027008191 6.9632410
3: AD Ex 18 11 7037 1579 0.002557908 0.0069664345 2.7234888 0.0131224789049098 0.1574697
4: AD In 23 6 7037 1579 0.003268438 0.0037998733 1.1625960 0.929880747744654 11.1585690
5: CE Ex 113 10 105508 13115 0.001071009 0.0007624857 0.7119322 0.373174639139558 4.4780957
6: CE In 109 18 105508 13115 0.001033097 0.0013724743 1.3285047 0.328102827641871 3.9372339
7: RI Ex 18 10 7849 2008 0.002293286 0.0049800797 2.1715914 0.0756378664437087 0.9076544
8: RI In 15 6 7849 2008 0.001911071 0.0029880478 1.5635458 0.508860550818325 6.1063266
9: TE Ex 310 28 58755 5848 0.005276147 0.0047879617 0.9074732 0.692122857490657 8.3054743
10: TE In 334 25 58755 5848 0.005684623 0.0042749658 0.7520228 0.199217416389958 2.3906090
11: TS Ex 156 61 37846 17028 0.004121968 0.0035823350 0.8690837 0.392722043288542 4.7126645
12: TS In 143 67 37846 17028 0.003778471 0.0039346958 1.0413461 0.842715736879803 10.1125888
human.dotplot <- splice_node_dot_plot2("./KCL/MicroExonator/Control_vs_KCL.diff.upstream_100nt.G4s", "./KCL/MicroExonator/Control_vs_KCL.diff.downstream_100nt.G4s" )
human.motif <- splice_node_dot_plot3("./KCL/MicroExonator/closest/Control_vs_KCL.diff.upstream.G4s",
"./KCL/MicroExonator/closest/Control_vs_KCL.diff.downstream.G4s",
100)
human.K <- splice_node_dot_plot3("./KCL/MicroExonator/closest/Control_vs_KCL.diff.upstream.G4seq_K",
"./KCL/MicroExonator/closest/Control_vs_KCL.diff.downstream.G4seq_K",
45)
human.PDS <- splice_node_dot_plot3("./KCL/MicroExonator/closest/Control_vs_KCL.diff.upstream.G4seq_PDS",
"./KCL/MicroExonator/closest/Control_vs_KCL.diff.downstream.G4seq_PDS",
45)
human.motif[ , G4_signal:="Motif" ]
human.K[ , G4_signal:="K+" ]
human.PDS[ , G4_signal:="PDS" ]
human.motif_K_PDS <- rbind(human.motif, human.K, human.PDS)
human.motif_K_PDS$G4_signal <- factor(human.motif_K_PDS$G4_signal, levels = c("Motif", "K+", "PDS") )
Fig5.A1 <- ggplot(human.motif_K_PDS) +
geom_point(aes(Type, diff, size = -log10(P_value.Bonferroni), shape=P_value.Bonferroni<0.05, colour=log2(OR) ) ) +
scale_colour_gradient2(low="blue", high="red", mid = "grey", midpoint = 0) +
facet_grid(G4_signal ~ .) +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
supp.dotplot.A <- splice_node_dot_plot2("./KCL/MicroExonator/ESC-derived_neuron_CD1.diff.upstream_100nt.G4s", "./KCL/MicroExonator/ESC-derived_neuron_CD1.diff.downstream_100nt.G4s" )
ESC_derived_neuron_CD1.motif <- splice_node_dot_plot3("./KCL/MicroExonator/closest/ESC-derived_neuron_CD1.diff.upstream.G4s.fix",
"./KCL/MicroExonator/closest/ESC-derived_neuron_CD1.diff.downstream.G4s.fix",
100)
Chi-squared approximation may be incorrect
ESC_derived_neuron_CD1.K <- splice_node_dot_plot3("./KCL/MicroExonator/closest/ESC-derived_neuron_CD1.diff.upstream.G4seq_K",
"./KCL/MicroExonator/closest/ESC-derived_neuron_CD1.diff.downstream.G4seq_K",
45)
Chi-squared approximation may be incorrectChi-squared approximation may be incorrectChi-squared approximation may be incorrectChi-squared approximation may be incorrectChi-squared approximation may be incorrect
ESC_derived_neuron_CD1.PDS <- splice_node_dot_plot3("./KCL/MicroExonator/closest/ESC-derived_neuron_CD1.diff.upstream.G4seq_PDS",
"./KCL/MicroExonator/closest/ESC-derived_neuron_CD1.diff.downstream.G4seq_PDS",
45)
ESC_derived_neuron_CD1.motif[ , G4_signal:="Motif" ]
ESC_derived_neuron_CD1.K[ , G4_signal:="K+" ]
ESC_derived_neuron_CD1.PDS[ , G4_signal:="PDS" ]
ESC_derived_neuron_CD1.motif_K_PDS <- rbind(ESC_derived_neuron_CD1.motif, ESC_derived_neuron_CD1.K, ESC_derived_neuron_CD1.PDS)
ESC_derived_neuron_CD1.motif_K_PDS$G4_signal <- factor(ESC_derived_neuron_CD1.motif_K_PDS$G4_signal, levels = c("Motif", "K+", "PDS") )
ggplot(ESC_derived_neuron_CD1.motif_K_PDS) +
geom_point(aes(Type, diff, size = -log10(P_value.Bonferroni), shape=P_value.Bonferroni<0.05, colour=log2(OR) ) ) +
scale_colour_gradient2(low="blue", high="red", mid = "grey", midpoint = 0) +
facet_grid(G4_signal ~ .) +
ylab("") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
supp.dotplot.C <- splice_node_dot_plot2("./KCL/MicroExonator/primary_cortical_neuron_DIV10_CD1.diff.upstream_100nt.G4s", "./KCL/MicroExonator/primary_cortical_neuron_DIV10_CD1.diff.downstream_100nt.G4s" )
primary_cortical_neuron_DIV10_CD1.motif <- splice_node_dot_plot3("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_CD1.diff.upstream.G4s.fix",
"./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_CD1.diff.downstream.G4s.fix",
100)
primary_cortical_neuron_DIV10_CD1.K <- splice_node_dot_plot3("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_CD1.diff.upstream.G4seq_K",
"./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_CD1.diff.downstream.G4seq_K",
45)
Chi-squared approximation may be incorrectChi-squared approximation may be incorrectChi-squared approximation may be incorrect
primary_cortical_neuron_DIV10_CD1.PDS <- splice_node_dot_plot3("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_CD1.diff.upstream.G4seq_PDS",
"./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_CD1.diff.downstream.G4seq_PDS",
45)
primary_cortical_neuron_DIV10_CD1.motif[ , G4_signal:="Motif" ]
primary_cortical_neuron_DIV10_CD1.K[ , G4_signal:="K+" ]
primary_cortical_neuron_DIV10_CD1.PDS[ , G4_signal:="PDS" ]
primary_cortical_neuron_DIV10_CD1.motif_K_PDS <- rbind(primary_cortical_neuron_DIV10_CD1.motif, primary_cortical_neuron_DIV10_CD1.K, primary_cortical_neuron_DIV10_CD1.PDS)
primary_cortical_neuron_DIV10_CD1.motif_K_PDS$G4_signal <- factor(primary_cortical_neuron_DIV10_CD1.motif_K_PDS$G4_signal, levels = c("Motif", "K+", "PDS") )
ggplot(primary_cortical_neuron_DIV10_CD1.motif_K_PDS) +
geom_point(aes(Type, diff, size = -log10(P_value.Bonferroni), shape=P_value.Bonferroni<0.05, colour=log2(OR) ) ) +
scale_colour_gradient2(low="blue", high="red", mid = "grey", midpoint = 0) +
facet_grid(G4_signal ~ .) +
ylab("") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
supp.dotplot.D <- splice_node_dot_plot2("./KCL/MicroExonator/primary_cortical_neuron_DIV10_Tc1.diff.upstream_100nt.G4s", "./KCL/MicroExonator/primary_cortical_neuron_DIV10_Tc1.diff.downstream_100nt.G4s" )
primary_cortical_neuron_DIV10_Tc1.motif <- splice_node_dot_plot3("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_Tc1.diff.upstream.G4s.fix",
"./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_Tc1.diff.downstream.G4s.fix",
100)
primary_cortical_neuron_DIV10_Tc1.K <- splice_node_dot_plot3("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_Tc1.diff.upstream.G4seq_K",
"./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_Tc1.diff.downstream.G4seq_K",
45)
primary_cortical_neuron_DIV10_Tc1.PDS <- splice_node_dot_plot3("./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_Tc1.diff.upstream.G4seq_PDS",
"./KCL/MicroExonator/closest/primary_cortical_neuron_DIV10_Tc1.diff.downstream.G4seq_PDS",
45)
primary_cortical_neuron_DIV10_Tc1.motif[ , G4_signal:="Motif" ]
primary_cortical_neuron_DIV10_Tc1.K[ , G4_signal:="K+" ]
primary_cortical_neuron_DIV10_Tc1.PDS[ , G4_signal:="PDS" ]
primary_cortical_neuron_DIV10_Tc1.motif_K_PDS <- rbind(primary_cortical_neuron_DIV10_Tc1.motif, primary_cortical_neuron_DIV10_Tc1.K, primary_cortical_neuron_DIV10_Tc1.PDS)
primary_cortical_neuron_DIV10_Tc1.motif_K_PDS$G4_signal <- factor(primary_cortical_neuron_DIV10_Tc1.motif_K_PDS$G4_signal, levels = c("Motif", "K+", "PDS") )
ggplot(primary_cortical_neuron_DIV10_Tc1.motif_K_PDS) +
geom_point(aes(Type, diff, size = -log10(P_value.Bonferroni), shape=P_value.Bonferroni<0.05, colour=log2(OR) ) ) +
scale_colour_gradient2(low="blue", high="red", mid = "grey", midpoint = 0) +
facet_grid(G4_signal ~ .) +
ylab("") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
KCL_human[(DeltaPsi<=-0.1 & Probability>0.9), Delta_type:="Included"]
KCL_human[(DeltaPsi>=0.1 & Probability>0.9), Delta_type:="Skiped"]
KCL_human[is.na(Delta_type), Delta_type:="None"]
KCL_human_stats <- KCL_human[Type=="CE" , .(count=.N), by=c("Delta_type", "exon", "G4_bol") ]
KCL_human_stats[, total:=sum(count), by="G4_bol"]
KCL_human_stats[, fraction:=count/total]
Fig5.B <- ggplot() +
geom_bar(data=KCL_human_stats[Delta_type!="None" & exon=="exon", ] , aes(x= G4_bol, y=fraction, group=Delta_type, fill=Delta_type ) , position="dodge", stat="identity" ) +
xlab("") +
ylab("Fraction of differentially inclued exons ") +
theme_bw() +
guides(fill=guide_legend(title="Alternative splicing event")) +
theme(legend.position = "top", legend.direction = "horizontal")
Fig5.B
diff.up <- read_dist_table("~/Google_Drive/Results/Non_B/KCL/SS_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.score.All_G4.tsv.clean.txt..bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.score.All_G4.tsv.clean.txt..bed.list.out.num'
diff.down <- read_dist_table("~/Google_Drive/Results/Non_B/KCL/SS_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.score.All_G4.tsv.clean.txt..bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.score.All_G4.tsv.clean.txt..bed.list.out.num'
eql.up <- read_dist_table("~/Google_Drive/Results/Non_B/KCL/SS_enrichment/Control_vs_KCL.diff_upstream_less.bed.score.All_G4.tsv.clean.txt..bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/Control_vs_KCL.diff_upstream_less.bed.score.All_G4.tsv.clean.txt..bed.list.out.num'
eql.down <- read_dist_table("~/Google_Drive/Results/Non_B/KCL/SS_enrichment/Control_vs_KCL.diff_downstream_less.bed.score.All_G4.tsv.clean.txt..bed.list.out.num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/Control_vs_KCL.diff_downstream_less.bed.score.All_G4.tsv.clean.txt..bed.list.out.num'
diff.up[, `:=`(type="diff", pos="up" )]
diff.down[, `:=`(type="diff", pos="down" )]
eql.up[, `:=`(type="eql", pos="up" )]
eql.down[, `:=`(type="eql", pos="down" )]
diff_eql <- rbind(diff.up, diff.down, eql.up, eql.down)
ggplot(diff_eql) +
geom_line(aes(x=Position, y=Enrrichment, group=type)) +
facet_grid(pos ~ .) +
theme_bw()
plot_eql_diff <- function(eql_up_plus, eql_up_minus, eql_down_plus, eql_down_minus, diff_up_plus, diff_up_minus, diff_down_plus, diff_down_minus ){
diff.up_plus <- read_dist_table(diff_up_plus)
diff.up_minus <- read_dist_table(diff_up_minus)
diff.down_plus <- read_dist_table(diff_down_plus)
diff.down_minus <- read_dist_table(diff_down_minus)
diff.up_minus[,Position:=Position*-1]
diff.down_minus[,Position:=Position*-1]
diff.TOTAL <- plot_density(diff.up_plus, diff.up_minus, diff.down_plus, diff.down_minus)
eql.up_plus <- read_dist_table(eql_up_plus)
eql.up_minus <- read_dist_table(eql_up_minus)
eql.down_plus <- read_dist_table(eql_down_plus)
eql.down_minus <- read_dist_table(eql_down_minus)
eql.up_minus[,Position:=Position*-1]
eql.down_minus[,Position:=Position*-1]
eql.TOTAL <- plot_density(eql.up_plus, eql.up_minus, eql.down_plus, eql.down_minus)
diff.TOTAL[, type:="diff"]
eql.TOTAL[, type:="eql"]
diff_eql.TOTAL <- rbind(diff.TOTAL, eql.TOTAL)
ggplot(diff_eql.TOTAL) +
geom_line(aes(x=Position, y=Enrrichment, color=type)) +
xlim(c(-250,250)) +
facet_grid(. ~ exon_pos ) +
labs(colour = "Potassium effect") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
}
plot_density_binomial <- function(up_plus, up_minus, down_plus, down_minus, observations, sig){
up_TOTAL <- merge(up_plus, up_minus, by="Position")
up_TOTAL[,Occurrences:=Occurrences.x+Occurrences.y]
up_TOTAL[,Occurrences:=Occurrences.x+Occurrences.y]
up_TOTAL <- cbind(up_TOTAL, up_TOTAL[, binconf(Occurrences, observations, alpha=sig) ])
up_TOTAL[,median:=median(PointEst)]
up_TOTAL[, Enrrichment:=PointEst/median]
up_TOTAL[, Enrrichment_l:=Lower/median]
up_TOTAL[, Enrrichment_u:=Upper/median]
up_TOTAL[, Position:=Position-1]
down_TOTAL <- merge(down_plus, down_minus, by="Position")
down_TOTAL[,Occurrences:=Occurrences.x+Occurrences.y]
down_TOTAL <- cbind(down_TOTAL, down_TOTAL[, binconf(Occurrences, observations, alpha=sig) ])
down_TOTAL[,median:=median(PointEst)]
down_TOTAL[, Enrrichment:=PointEst/median]
down_TOTAL[, Enrrichment_l:=Lower/median]
down_TOTAL[, Enrrichment_u:=Upper/median]
down_TOTAL[, Position:=Position-1]
up_TOTAL[ ,exon_pos:="Upstream"]
down_TOTAL[ ,exon_pos:="Downstream"]
TOTAL <- rbind(up_TOTAL, down_TOTAL)
TOTAL$exon_pos <- factor(TOTAL$exon_pos, levels=c("Upstream", "Downstream" ))
p <- ggplot(TOTAL)+
geom_line(aes(x=Position,y=Enrrichment)) +
geom_ribbon(aes(ymin=Enrrichment_l, ymax=Enrrichment_u, x=Position), alpha=0.3 )+
facet_grid( . ~ exon_pos ) +
theme_bw()
show(p)
return(TOTAL)
}
primary_cortical_neuron_DIV10_CD1.CE.NA
[1] 103907
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_upstream_less.bed.plus.score.All_G4.tsv.clean.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_upstream_less.bed.minus.score.All_G4.tsv.clean.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_downstream_less.bed.plus.score.All_G4.tsv.clean.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_downstream_less.bed.minus.score.All_G4.tsv.clean.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_upstream_prob_0_9.bed.plus.score.All_G4.tsv.clean.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_upstream_prob_0_9.bed.minus.score.All_G4.tsv.clean.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_downstream_prob_0_9.bed.plus.score.All_G4.tsv.clean.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_downstream_prob_0_9.bed.minus.score.All_G4.tsv.clean.txt..bed.list.out.num",
human.CE.NA,
human.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_upstream_prob_0_9.bed.plus.score.All_G4.tsv.clean.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_upstream_prob_0_9.bed.minus.score.All_G4.tsv.clean.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_downstream_prob_0_9.bed.plus.score.All_G4.tsv.clean.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/Control_vs_KCL.diff_downstream_prob_0_9.bed.minus.score.All_G4.tsv.clean.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_upstream_less.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_upstream_less.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_downstream_less.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_downstream_less.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num",
ESC_derived_neuron_CD1.CE.NA,
ESC_derived_neuron_CD1.CE.diff,
0.05)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_upstream_less.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_upstream_less.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_downstream_less.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_downstream_less.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num",
primary_cortical_neuron_DIV10_Tc1.CE.NA,
primary_cortical_neuron_DIV10_Tc1.CE.diff,
0.05)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_upstream_less.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_upstream_less.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_downstream_less.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_downstream_less.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num",
primary_cortical_neuron_DIV4_CD1.CE.NA,
primary_cortical_neuron_DIV4_CD1.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_upstream_less.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_upstream_less.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_downstream_less.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_downstream_less.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num",
primary_cortical_neuron_DIV10_CD1.CE.NA,
primary_cortical_neuron_DIV10_CD1.CE.diff,
0.05)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.plus.score.mm10.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/SS_enrichment/plus_minus/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.minus.score.mm10.txt..bed.list.out.num'
plot_eql_diff(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_less.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_less.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_less.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_less.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num"
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Fig5.C <- plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_less.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_less.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_less.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_less.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
human.CE.NA,
human.CE.diff,
0.05)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.plus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.minus.score.GSM3003539_Homo_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Fig5.c <- Fig5.C +ylim( c(0.4, 2.1))
Fig5.c
Fig5.D <- plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_less.bed.plus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_less.bed.minus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_less.bed.plus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_less.bed.minus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.plus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.minus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.plus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.minus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
human.CE.NA,
human.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.plus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_upstream_prob_0_9.bed.minus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.plus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/Control_vs_KCL.diff_downstream_prob_0_9.bed.minus.score.GSM3003540_Homo_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Fig5.D <- Fig5.D +ylim( c(0.4, 2.1))
Fig5.D
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_less.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_less.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_less.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_less.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
ESC_derived_neuron_CD1.CE.NA,
ESC_derived_neuron_CD1.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_less.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_less.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_less.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_less.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
ESC_derived_neuron_CD1.CE.NA,
ESC_derived_neuron_CD1.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/ESC-derived_neuron_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_less.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_less.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_less.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_less.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
primary_cortical_neuron_DIV10_CD1.CE.NA,
primary_cortical_neuron_DIV10_CD1.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_less.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_less.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_less.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_less.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
primary_cortical_neuron_DIV10_CD1.CE.NA,
primary_cortical_neuron_DIV10_CD1.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_less.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_less.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_less.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_less.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
primary_cortical_neuron_DIV10_Tc1.CE.NA,
primary_cortical_neuron_DIV10_Tc1.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_less.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_less.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_less.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_less.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
primary_cortical_neuron_DIV10_Tc1.CE.NA,
primary_cortical_neuron_DIV10_Tc1.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_upstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV10_Tc1.diff_downstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_less.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_less.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_less.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_less.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num",
primary_cortical_neuron_DIV4_CD1.CE.NA,
primary_cortical_neuron_DIV4_CD1.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003547_Mouse_all_w15_th-1_plus_minus.hits.max.K.w50.25.bed.txt..bed.list.out.num'
plot_eql_diff_binomial(
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_less.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_less.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_less.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_less.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
"~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num",
primary_cortical_neuron_DIV4_CD1.CE.NA,
primary_cortical_neuron_DIV4_CD1.CE.diff,
0.05
)
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_upstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.plus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/KCL/G4seq_enrichment/primary_cortical_neuron_DIV4_CD1.diff_downstream_prob_0_9.bed.minus.score.GSM3003548_Mouse_all_w15_th-1_plus_minus.hits.max.PDS.w50.35.bed.txt..bed.list.out.num'
rep(1:1999, each=4)
[1] 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 5 5 5 5 6 6 6 6 7 7 7 7 8 8 8 8 9 9 9 9 10 10 10 10 11 11 11 11 12 12
[47] 12 12 13 13 13 13 14 14 14 14 15 15 15 15 16 16 16 16 17 17 17 17 18 18 18 18 19 19 19 19 20 20 20 20 21 21 21 21 22 22 22 22 23 23 23 23
[93] 24 24 24 24 25 25 25 25 26 26 26 26 27 27 27 27 28 28 28 28 29 29 29 29 30 30 30 30 31 31 31 31 32 32 32 32 33 33 33 33 34 34 34 34 35 35
[139] 35 35 36 36 36 36 37 37 37 37 38 38 38 38 39 39 39 39 40 40 40 40 41 41 41 41 42 42 42 42 43 43 43 43 44 44 44 44 45 45 45 45 46 46 46 46
[185] 47 47 47 47 48 48 48 48 49 49 49 49 50 50 50 50 51 51 51 51 52 52 52 52 53 53 53 53 54 54 54 54 55 55 55 55 56 56 56 56 57 57 57 57 58 58
[231] 58 58 59 59 59 59 60 60 60 60 61 61 61 61 62 62 62 62 63 63 63 63 64 64 64 64 65 65 65 65 66 66 66 66 67 67 67 67 68 68 68 68 69 69 69 69
[277] 70 70 70 70 71 71 71 71 72 72 72 72 73 73 73 73 74 74 74 74 75 75 75 75 76 76 76 76 77 77 77 77 78 78 78 78 79 79 79 79 80 80 80 80 81 81
[323] 81 81 82 82 82 82 83 83 83 83 84 84 84 84 85 85 85 85 86 86 86 86 87 87 87 87 88 88 88 88 89 89 89 89 90 90 90 90 91 91 91 91 92 92 92 92
[369] 93 93 93 93 94 94 94 94 95 95 95 95 96 96 96 96 97 97 97 97 98 98 98 98 99 99 99 99 100 100 100 100 101 101 101 101 102 102 102 102 103 103 103 103 104 104
[415] 104 104 105 105 105 105 106 106 106 106 107 107 107 107 108 108 108 108 109 109 109 109 110 110 110 110 111 111 111 111 112 112 112 112 113 113 113 113 114 114 114 114 115 115 115 115
[461] 116 116 116 116 117 117 117 117 118 118 118 118 119 119 119 119 120 120 120 120 121 121 121 121 122 122 122 122 123 123 123 123 124 124 124 124 125 125 125 125 126 126 126 126 127 127
[507] 127 127 128 128 128 128 129 129 129 129 130 130 130 130 131 131 131 131 132 132 132 132 133 133 133 133 134 134 134 134 135 135 135 135 136 136 136 136 137 137 137 137 138 138 138 138
[553] 139 139 139 139 140 140 140 140 141 141 141 141 142 142 142 142 143 143 143 143 144 144 144 144 145 145 145 145 146 146 146 146 147 147 147 147 148 148 148 148 149 149 149 149 150 150
[599] 150 150 151 151 151 151 152 152 152 152 153 153 153 153 154 154 154 154 155 155 155 155 156 156 156 156 157 157 157 157 158 158 158 158 159 159 159 159 160 160 160 160 161 161 161 161
[645] 162 162 162 162 163 163 163 163 164 164 164 164 165 165 165 165 166 166 166 166 167 167 167 167 168 168 168 168 169 169 169 169 170 170 170 170 171 171 171 171 172 172 172 172 173 173
[691] 173 173 174 174 174 174 175 175 175 175 176 176 176 176 177 177 177 177 178 178 178 178 179 179 179 179 180 180 180 180 181 181 181 181 182 182 182 182 183 183 183 183 184 184 184 184
[737] 185 185 185 185 186 186 186 186 187 187 187 187 188 188 188 188 189 189 189 189 190 190 190 190 191 191 191 191 192 192 192 192 193 193 193 193 194 194 194 194 195 195 195 195 196 196
[783] 196 196 197 197 197 197 198 198 198 198 199 199 199 199 200 200 200 200 201 201 201 201 202 202 202 202 203 203 203 203 204 204 204 204 205 205 205 205 206 206 206 206 207 207 207 207
[829] 208 208 208 208 209 209 209 209 210 210 210 210 211 211 211 211 212 212 212 212 213 213 213 213 214 214 214 214 215 215 215 215 216 216 216 216 217 217 217 217 218 218 218 218 219 219
[875] 219 219 220 220 220 220 221 221 221 221 222 222 222 222 223 223 223 223 224 224 224 224 225 225 225 225 226 226 226 226 227 227 227 227 228 228 228 228 229 229 229 229 230 230 230 230
[921] 231 231 231 231 232 232 232 232 233 233 233 233 234 234 234 234 235 235 235 235 236 236 236 236 237 237 237 237 238 238 238 238 239 239 239 239 240 240 240 240 241 241 241 241 242 242
[967] 242 242 243 243 243 243 244 244 244 244 245 245 245 245 246 246 246 246 247 247 247 247 248 248 248 248 249 249 249 249 250 250 250 250
[ reached getOption("max.print") -- omitted 6996 entries ]
diff_eql.TOTAL[ , bin:=rep(1:1999, each=4) ]
diff_eql.TOTAL[, mean_Enrrichment:=mean(Enrrichment) , by=bin]
ggplot(diff_eql.TOTAL) +
geom_line(aes(x=Position, y=mean_Enrrichment, color=type)) +
xlim(c(-250,250)) +
facet_grid(. ~ exon_pos ) +
labs(colour = "Potassium effect") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal")
ks.test(intron_size[G4>0, intron_size], intron_size[G4==0, intron_size])
p-value will be approximate in the presence of ties
Two-sample Kolmogorov-Smirnov test
data: intron_size[G4 > 0, intron_size] and intron_size[G4 == 0, intron_size]
D = 0.25781, p-value < 2.2e-16
alternative hypothesis: two-sided
size_int <- c(seq(0,5000,10), c(10000, 100000, 1000000, 10000000))
intron_size$int_count <- cut(intron_size$intron_size, size_int)
int_counts_up_w_G4 <- table(intron_size[pos=="Upstream intron" & G4>0, ]$int_count)
int_counts_up_wo_G4 <- table(intron_size[pos=="Upstream intron" & G4==0, ]$int_count)
int_counts_up <- rbind(int_counts_up_w_G4, int_counts_up_wo_G4)
colnames(int_counts_up) <- c(seq(10,5000,10), c(10000, 100000, 1000000, 10000000))
int_counts_up <- melt(int_counts_up)
int_counts_down_w_G4 <- table(intron_size[pos=="Downstream intron" & G4>0, ]$int_count)
int_counts_down_wo_G4 <- table(intron_size[pos=="Downstream intron" & G4==0, ]$int_count)
int_counts_down <- rbind(int_counts_down_w_G4, int_counts_down_wo_G4)
colnames(int_counts_down) <- c(seq(10,5000,10), c(10000, 100000, 1000000, 10000000))
int_counts_down <- melt(int_counts_down)
intron_size_ints <- rbind(int_counts_up, int_counts_down)
colnames(intron_size_ints) <- c("factor", "int", "count")
intron_size_ints <- data.table(intron_size_ints)
intron_size_ints[ , total:=sum(count) , by="factor" ]
intron_size_ints[ , frac:=(count/total) ]
intron_size_ints_up <- merge(intron_size_ints[ factor=="int_counts_up_w_G4", ], intron_size_ints[ factor=="int_counts_up_wo_G4", ], by="int" )
intron_size_ints_up[ , relative_frac:=frac.x/frac.y ]
intron_size_ints_down <- merge(intron_size_ints[ factor=="int_counts_down_w_G4", ], intron_size_ints[ factor=="int_counts_down_wo_G4", ], by="int" )
intron_size_ints_down[ , relative_frac:=frac.x/frac.y ]
intron_size_ints_up[, pos:="Upstream intron"]
intron_size_ints_down[, pos:="Downstream intron"]
intron_size_ints_total <- rbind(intron_size_ints_up, intron_size_ints_down)
intron_size_ints_total$pos <- factor(intron_size_ints_total$pos, level=c("Upstream intron", "Downstream intron"))
Fig3.C <- ggplot(intron_size_ints_total, aes(int, log2(relative_frac)) ) +
geom_hline(yintercept=0, linetype="dashed") +
geom_point() +
stat_smooth( method = "lm", formula = y ~ poly(x, 8)) +
xlim(c(0, 2000)) +
ylim(c(-2,2)) +
facet_grid(. ~ pos)
Fig3.C
intron_size_ints_total[ relative_frac %in% intron_size_ints_total[, max(relative_frac), by=pos]$V1, ]
int factor.x count.x total.x frac.x factor.y count.y total.y frac.y relative_frac pos
1: 70 int_counts_up_w_G4 150 61795 0.002427381 int_counts_up_wo_G4 509 651213 0.0007816183 3.105583 Upstream intron
2: 70 int_counts_down_w_G4 150 42311 0.003545177 int_counts_down_wo_G4 509 670697 0.0007589120 4.671395 Downstream intron
Upstream_U2_score_len <- fread("./Figures/Figure3/Upstream_U2_score_len_matrix.txt2.old")
Downstream_U2_score_len <- fread("./Figures/Figure3/Downstream_U2_score_len_matrix.txt2.old")
Upstream_U2_score_len <-data.table::melt(Upstream_U2_score_len, id.vars='IL')
Downstream_U2_score_len <- data.table::melt(Downstream_U2_score_len, id.vars='IL')
Upstream_U2_score_len[, pos:="Upstream intron"]
Downstream_U2_score_len[, pos:="Downstream intron"]
Fig3.D1 <- ggplot(Upstream_U2_score_len) +
geom_tile( aes(variable, as.factor(IL), fill = value*100)) +
scale_fill_gradient2(low="blue", high="red", mid = "grey", midpoint = 12.5, limits = c(0, 25)) +
facet_grid(. ~ pos) +
theme(legend.position = "bottom", legend.direction = "horizontal") + theme(axis.text.x = element_text(angle = 90)) +labs(x = NULL, y = NULL)
Fig3.D2 <- ggplot(Downstream_U2_score_len) +
geom_tile( aes(variable, as.factor(IL), fill = value*100)) +
scale_fill_gradient2(low="blue", high="red", mid = "grey", midpoint = 12.5, limits = c(0, 25)) +
facet_grid(. ~ pos) +
theme(legend.position = "bottom", legend.direction = "horizontal") +
theme(legend.position = "bottom", legend.direction = "horizontal") + theme(axis.text.x = element_text(angle = 90)) +labs(x = NULL, y = NULL)
Fig3.D <- plot_grid(Fig3.D1, Fig3.D2)
Fig3.D
closest_g4 <- function(dist.exon_up_plus_path, dist.exon_up_minus_path, dist.exon_down_plus_path, dist.exon_down_minus_path){
dist.exon_up_plus <- fread(dist.exon_up_plus_path)
colnames(dist.exon_up_plus) <- c("echrom", "estart", "eend", "exon", "cero", "strand", "gchrom", "gstart", "gend", "gscore", "exon_dist")
dist.exon_up_plus[, gmid:= gstart + (gend-gstart)/2]
dist.exon_up_plus[ , dist:=gmid - estart]
dist.exon_up_minus <- fread(dist.exon_up_minus_path)
colnames(dist.exon_up_minus) <- c("echrom", "estart", "eend", "exon", "cero", "strand", "gchrom", "gstart", "gend", "gscore", "exon_dist")
dist.exon_up_minus[, gmid:= gstart + (gend-gstart)/2]
dist.exon_up_minus[ , dist:= estart - gmid]
dist.exon_down_plus <- fread(dist.exon_down_plus_path)
colnames(dist.exon_down_plus) <- c("echrom", "estart", "eend", "exon", "cero", "strand", "gchrom", "gstart", "gend", "gscore", "exon_dist")
dist.exon_down_plus[, gmid:= gstart + (gend-gstart)/2]
dist.exon_down_plus[ , dist:=gmid - estart]
dist.exon_down_minus <- fread(dist.exon_down_minus_path)
colnames(dist.exon_down_minus) <- c("echrom", "estart", "eend", "exon", "cero", "strand", "gchrom", "gstart", "gend", "gscore", "exon_dist")
dist.exon_down_minus[, gmid:= gstart + (gend-gstart)/2]
dist.exon_down_minus[ , dist:= estart - gmid]
dist.exon_up <- rbind(dist.exon_up_plus, dist.exon_up_minus)
dist.exon_down <- rbind(dist.exon_down_plus, dist.exon_down_minus)
dist.exon_up[, pos:="3'Splice site"]
dist.exon_down[, pos:="5'Splice site"]
dist.exon <- rbind(dist.exon_up, dist.exon_down)
return(dist.exon)
}
exon.up.motif <- fread("./Figures/Figure1/exons.up.closest_G4_clean")
colnames(exon.up.motif) <- c("echrom", "estart", "eend", "exon", "cero", "strand", "gchrom", "gstart", "gend")
exon.up.motif[ , gmid:= gstart + (gend-gstart)/2]
exon.up.motif[ strand=="+" , dist:=gmid - estart]
exon.up.motif[ strand=="-" , dist:= estart - gmid]
exon.down.motif <- fread("./Figures/Figure1/exons.down.closest_G4_clean")
colnames(exon.down.motif) <- c("echrom", "estart", "eend", "exon", "cero", "strand", "gchrom", "gstart", "gend")
exon.down.motif[ , gmid:= gstart + (gend-gstart)/2]
exon.down.motif[ strand=="+" , dist:=gmid - estart]
exon.down.motif[ strand=="-" , dist:= estart - gmid]
exon.up.motif[, pos:="3'Splice site"]
exon.down.motif[, pos:="5'Splice site"]
exon.dist.motif <- rbind(exon.up.motif, exon.down.motif)
ggplot(exon.dist.motif) +
geom_density(aes(dist)) +
xlim(c(-1000, 1000)) +
facet_grid(. ~ pos)
NA
Fig1.B + xlim(c(-300, 300))
Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
closest_g4_2015 <- function(dist.exon_up_plus_path, dist.exon_up_minus_path, dist.exon_down_plus_path, dist.exon_down_minus_path){
dist.exon_up_plus <- fread(dist.exon_up_plus_path)
colnames(dist.exon_up_plus) <- c("echrom", "estart", "eend", "exon", "cero", "strand", "gchrom", "gstart", "gend", "exon_dist")
dist.exon_up_plus[, gmid:= gstart + (gend-gstart)/2]
dist.exon_up_plus[ , dist:=gmid - estart]
dist.exon_up_minus <- fread(dist.exon_up_minus_path)
colnames(dist.exon_up_minus) <- c("echrom", "estart", "eend", "exon", "cero", "strand", "gchrom", "gstart", "gend", "exon_dist")
dist.exon_up_minus[, gmid:= gstart + (gend-gstart)/2]
dist.exon_up_minus[ , dist:= estart - gmid]
dist.exon_down_plus <- fread(dist.exon_down_plus_path)
colnames(dist.exon_down_plus) <- c("echrom", "estart", "eend", "exon", "cero", "strand", "gchrom", "gstart", "gend", "exon_dist")
dist.exon_down_plus[, gmid:= gstart + (gend-gstart)/2]
dist.exon_down_plus[ , dist:=gmid - estart]
dist.exon_down_minus <- fread(dist.exon_down_minus_path)
colnames(dist.exon_down_minus) <- c("echrom", "estart", "eend", "exon", "cero", "strand", "gchrom", "gstart", "gend", "exon_dist")
dist.exon_down_minus[, gmid:= gstart + (gend-gstart)/2]
dist.exon_down_minus[ , dist:= estart - gmid]
dist.exon_up <- rbind(dist.exon_up_plus, dist.exon_up_minus)
dist.exon_down <- rbind(dist.exon_down_plus, dist.exon_down_minus)
dist.exon_up[, pos:="3'Splice site"]
dist.exon_down[, pos:="5'Splice site"]
dist.exon <- rbind(dist.exon_up, dist.exon_down)
return(dist.exon)
}
closest_g4_KCL_2015 <- closest_g4_2015("./Figures/Figure1/exon_up_plus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed",
"Figures/Figure1/exon_up_minus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed",
"Figures/Figure1/exon_down_plus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed",
"Figures/Figure1/exon_down_minus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed")
closest_g4_PDS_2015 <- closest_g4_2015("./Figures/Figure1/exon_up_plus.hg19.closest.GSE63874_Na_PDS_plus_minus_hits_intersect.bed",
"Figures/Figure1/exon_up_minus.hg19.closest.GSE63874_Na_PDS_plus_minus_hits_intersect.bed",
"Figures/Figure1/exon_down_plus.hg19.closest.GSE63874_Na_PDS_plus_minus_hits_intersect.bed",
"Figures/Figure1/exon_down_minus.hg19.closest.GSE63874_Na_PDS_plus_minus_hits_intersect.bed")
closest_g4_KCL_2015[, Type:="G4-seq Na+ K+"]
closest_g4_PDS_2015[, Type:="G4-seq Na+ PDS"]
closest_g4_KCL_2015 <- unique(closest_g4_KCL_2015[ , c("echrom", "estart", "eend", "dist", "pos", "Type")])
closest_g4_PDS_2015 <- unique(closest_g4_PDS_2015[ , c("echrom", "estart", "eend", "dist", "pos", "Type")])
closest_g4_KCL_PDS_2015 <- rbind(closest_g4_KCL_2015, closest_g4_PDS_2015)
ggplot(closest_g4_KCL_PDS_2015) +
geom_line(aes(dist, colour=Type), bw=10, stat="density") +
xlim(c(-1000, 1000)) +
facet_grid(Type ~ pos) +
xlab("Distance") +
ylab("Density") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal") +
theme(axis.text.x = element_text( angle = 45))
closest_g4.TOTAL.1kb <- closest_g4.TOTAL[abs(dist)<=1000 , ]
closest_g4.TOTAL.1kb[, bin:=cut(dist, seq(-1000, 1000, 5), labels= seq(-995, 1000, 5) ) ]
closest_g4.TOTAL.1kb.enrichment <- closest_g4.TOTAL.1kb[ , .(Occurrences=.N) , by=c("bin", "pos", "Treatment", "Species")]
closest_g4.TOTAL.1kb.enrichment.median <- closest_g4.TOTAL.1kb.enrichment[, .(median=median(Occurrences)), by=c( "pos", "Treatment", "Species") ]
closest_g4.TOTAL.1kb.enrichment <- merge(closest_g4.TOTAL.1kb.enrichment, closest_g4.TOTAL.1kb.enrichment.median, by=c( "pos", "Treatment", "Species"))
closest_g4.TOTAL.1kb.enrichment[, Enrrichment:=Occurrences/median]
closest_g4.TOTAL.1kb.enrichment[ , bin:=as.numeric(as.character(bin))]
Fig6.D <- ggplot(closest_g4.TOTAL.1kb.enrichment) +
geom_line(aes(bin, Enrrichment, colour=Species)) +
xlim(c(-1000, 1000)) +
facet_grid(Treatment ~ pos) +
xlab("Distance") +
ylab("Enrichment") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal") +
theme(axis.text.x = element_text(vjust = 0.7,
angle = 45))
Fig6.D
read_dist_table_plus_minus <- function(path.plus, path.minus ){
dist_table.plus <- data.table(read_delim(path.plus,
"\t", escape_double = FALSE, col_names = FALSE,
trim_ws = TRUE))
dist_table.plus <- dist_table.plus[, 2:2001]
dist_table.plus <- data.table(as.data.frame(t(dist_table.plus)))
colnames(dist_table.plus) <- c("Position", "Occurrences")
dist_table.minus <- data.table(read_delim(path.minus,
"\t", escape_double = FALSE, col_names = FALSE,
trim_ws = TRUE))
dist_table.minus <- dist_table.minus[, 2:2001]
dist_table.minus <- data.table(as.data.frame(t(dist_table.minus)))
colnames(dist_table.minus) <- c("Position", "Occurrences")
dist_table <- merge(dist_table.plus, dist_table.minus, by="Position")
dist_table[, Occurrences:=(Occurrences.x + Occurrences.y)]
dist_table[, Occurrences:=(Occurrences.x + Occurrences.y)]
dist_table <- dist_table[, c("Position", "Occurrences")]
dist_table[,median:=median(Occurrences)]
dist_table[, Enrrichment:=Occurrences/median]
dist_table[, Position:=Position-1]
return(dist_table)
}
enrichment_G4_seq_plot <- function(path.up_plus.plus, path.up_plus.minus,
path.down_plus.plus, path.down_plus.minus,
path.up_minus.plus, path.up_minus.minus,
path.down_minus.plus, path.down_minus.minus ){
x.up_plus <- read_dist_table_plus_minus(path.up_plus.plus,
path.up_plus.minus)
x.down_plus <- read_dist_table_plus_minus(path.down_plus.plus,
path.down_plus.minus)
x.up_minus <- read_dist_table_plus_minus(path.up_minus.plus,
path.up_minus.minus)
x.down_minus <- read_dist_table_plus_minus(path.down_minus.plus,
path.down_minus.minus)
x.up_minus[,Position:=Position*-1]
x.down_minus[,Position:=Position*-1]
x.TOTAL <- plot_density(x.up_plus, x.up_minus, x.down_plus, x.down_minus)
return(x.TOTAL)
}
hg19.TOTAL.KCL <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.hg19.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.hg19.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.hg19.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.hg19.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.hg19.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.hg19.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.hg19.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.hg19.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.hg19.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.hg19.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.hg19.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.hg19.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.hg19.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.hg19.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.hg19.score.GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.hg19.score.GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
hg19.TOTAL.PDS <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.hg19.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.hg19.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.hg19.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.hg19.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.hg19.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.hg19.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.hg19.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.hg19.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.hg19.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.hg19.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.hg19.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.hg19.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.hg19.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.hg19.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.hg19.score.GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.hg19.score.GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
sacCer3.TOTAL.KCL <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.sacCer3.score.GSM3003553_Saccaromyces_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
sacCer3.TOTAL.PDS <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.sacCer3.score.GSM3003554_Saccaromyces_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
mouse.TOTAL.KCL <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.mm10.score.GSM3003547_Mouse_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.mm10.score.GSM3003547_Mouse_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.mm10.score.GSM3003547_Mouse_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.mm10.score.GSM3003547_Mouse_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.mm10.score.GSM3003547_Mouse_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.mm10.score.GSM3003547_Mouse_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.mm10.score.GSM3003547_Mouse_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.mm10.score.GSM3003547_Mouse_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.mm10.score.GSM3003547_Mouse_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.mm10.score.GSM3003547_Mouse_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.mm10.score.GSM3003547_Mouse_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.mm10.score.GSM3003547_Mouse_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.mm10.score.GSM3003547_Mouse_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.mm10.score.GSM3003547_Mouse_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.mm10.score.GSM3003547_Mouse_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.mm10.score.GSM3003547_Mouse_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
mouse.TOTAL.PDS <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.mm10.score.GSM3003548_Mouse_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.mm10.score.GSM3003548_Mouse_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.mm10.score.GSM3003548_Mouse_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.mm10.score.GSM3003548_Mouse_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.mm10.score.GSM3003548_Mouse_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.mm10.score.GSM3003548_Mouse_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.mm10.score.GSM3003548_Mouse_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.mm10.score.GSM3003548_Mouse_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.mm10.score.GSM3003548_Mouse_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.mm10.score.GSM3003548_Mouse_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.mm10.score.GSM3003548_Mouse_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.mm10.score.GSM3003548_Mouse_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.mm10.score.GSM3003548_Mouse_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.mm10.score.GSM3003548_Mouse_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.mm10.score.GSM3003548_Mouse_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.mm10.score.GSM3003548_Mouse_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
dm6.TOTAL.KCL <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.dm6.score.GSM3003541_Drosophila_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
dm6.TOTAL.PDS <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.dm6.score.GSM3003542_Drosophila_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
tair10.TOTAL.KCL <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed_tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed_tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed_tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed_tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.tair10.score.GSM3003535_Arabidopsis_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
tair10.TOTAL.PDS <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed_tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed_tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed_tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.bed_tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.bed.tair10.score.GSM3003536_Arabidopsis_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
danRer10.TOTAL.KCL <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_plus.hits.max.K.w50.25.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.danRer10.score.GSM3003557_Zebrafish_all_w15_th-1_minus.hits.max.K.w50.25.bed.txt..num'
danRer10.TOTAL.PDS <- enrichment_G4_seq_plot("~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num",
"~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num")
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_plus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_plus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_up_minus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.txt..num'
Parsed with column specification:
cols(
.default = col_double()
)
See spec(...) for full column specifications.
1 parsing failure.
row col expected actual file
2 -- 2001 columns 2002 columns '~/Google_Drive/Results/Non_B/G4_seq_2019/Evolution/exon_down_minus.danRer10.score.GSM3003558_Zebrafish_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.txt..num'
hg19.TOTAL.KCL[, Treatment:="KCl"]
hg19.TOTAL.PDS[, Treatment:="PDS"]
hg19.TOTAL.KCL[, Species:="H. sapiens"]
hg19.TOTAL.PDS[, Species:="H. sapiens"]
sacCer3.TOTAL.KCL[, Treatment:="KCl"]
sacCer3.TOTAL.PDS[, Treatment:="PDS"]
sacCer3.TOTAL.KCL[, Species:="S. cerevisiae"]
sacCer3.TOTAL.PDS[, Species:="S. cerevisiae"]
mouse.TOTAL.KCL[, Treatment:="KCl"]
mouse.TOTAL.PDS[, Treatment:="PDS"]
mouse.TOTAL.KCL[, Species:="M. musculus"]
mouse.TOTAL.PDS[, Species:="M. musculus"]
dm6.TOTAL.KCL[, Treatment:="KCl"]
dm6.TOTAL.PDS[, Treatment:="PDS"]
dm6.TOTAL.KCL[, Species:="D. melanogaster"]
dm6.TOTAL.PDS[, Species:="D. melanogaster"]
tair10.TOTAL.KCL[, Treatment:="KCl"]
tair10.TOTAL.PDS[, Treatment:="PDS"]
tair10.TOTAL.KCL[, Species:="A. thaliana"]
tair10.TOTAL.PDS[, Species:="A. thaliana"]
danRer10.TOTAL.KCL[, Treatment:="KCl"]
danRer10.TOTAL.PDS[, Treatment:="PDS"]
danRer10.TOTAL.KCL[, Species:="D. rerio"]
danRer10.TOTAL.PDS[, Species:="D. rerio"]
TOTAL.KCL_PDS <- rbind(hg19.TOTAL.KCL, hg19.TOTAL.PDS, sacCer3.TOTAL.KCL, sacCer3.TOTAL.PDS, mouse.TOTAL.KCL, mouse.TOTAL.PDS, dm6.TOTAL.KCL, dm6.TOTAL.PDS, tair10.TOTAL.KCL, tair10.TOTAL.PDS, danRer10.TOTAL.KCL, danRer10.TOTAL.PDS)
ggplot(TOTAL.KCL_PDS) +
geom_line(aes(Position, Enrrichment, colour=Species)) +
xlim(c(-1000, 1000)) +
facet_grid(Treatment ~ exon_pos) +
xlab("Distance") +
ylab("Enrichment") +
theme_bw() +
theme(legend.position = "top", legend.direction = "horizontal") +
theme(axis.text.x = element_text(vjust = 0.7,
angle = 45))
closest_g4_KCL.hg19.2015 <- closest_g4("./Figures/Supplementary/exon_up_plus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed",
"Figures/Supplementary/exon_up_minus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed",
"Figures/Supplementary/exon_down_plus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed",
"Figures/Supplementary/exon_down_minus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed")
closest_g4_KCL.hg19.2015 <- closest_g4("./Figures/Supplementary/exon_up_plus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed",
"Figures/Supplementary/exon_up_minus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed",
"Figures/Supplementary/exon_down_plus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed",
"Figures/Supplementary/exon_down_minus.hg19.closest.GSE63874_Na_K_plus_minus_hits_intersect.bed")
KCL_up <- unique(closest_g4_KCL[abs(dist)>=100 & pos=="3'Splice site", paste(echrom, estart, eend, sep = "_")])
gg_color_hue <- function(n) {
hues = seq(15, 375, length = n + 1)
hcl(h = hues, l = 65, c = 100)[1:n]
}
gg_color_hue(3)
[1] "#F8766D" "#00BA38" "#619CFF"
library(eulerr)
VennDiag.up <- euler(c("Motif" = 8807+9325,
"K" = 9653+10029,
"PDS" = 34880+36909,
"K&PDS" = 9890+9539,
"PDS&Motif" = 8331+8855,
"K&Motif" = 4509+4749,
"K&PDS&Motif" = 4503+4747))
Fig1.C1 <- plot(VennDiag.up, counts = TRUE, font=2, cex=1, alpha=0.5,
fill=gg_color_hue(3), quantities = list(fontsize = 10))
VennDiag.down <- euler(c("Motif" = 9507+10142,
"K" = 10120+9365,
"PDS" = 34844+36737,
"K&PDS" = 9236+9985,
"PDS&Motif" = 8973+9593,
"K&Motif" = 4806+5221,
"K&PDS&Motif" = 4802+5211))
Fig1.C2 <- plot(VennDiag.down, counts = TRUE, font=1, cex=1, alpha=0.5,
fill=gg_color_hue(3), quantities = list(fontsize = 10))
Fig1.C <- plot_grid(Fig1.C1, Fig1.C2, nrow=1)
Fig1.C
VennDiag.up_2015 <- euler(c("Motif" = 18132,
"K" = 34761,
"PDS" = 50894,
"K&PDS" = 31711,
"PDS&Motif" = 14786,
"K&Motif" = 11794,
"K&PDS&Motif" = 11250))
venn_supp.up <- plot(VennDiag.up_2015, counts = TRUE, font=2, cex=1, alpha=0.5,
fill=gg_color_hue(3), quantities = list(fontsize = 10))
VennDiag.down_2015 <- euler(c("Motif" = 19649,
"K" = 33908,
"PDS" = 49806,
"K&PDS" = 30920,
"PDS&Motif" = 15951,
"K&Motif" = 12615,
"K&PDS&Motif" = 12027))
venn_supp.down <- plot(VennDiag.down_2015, counts = TRUE, font=1, cex=1, alpha=0.5,
fill=gg_color_hue(3), quantities = list(fontsize = 10))
plot_grid(venn_supp.up, venn_supp.down, labels = c("3' Splice site", "5' Splice site"))
dataframe_G4_consensus_motif_enrichment_species <- fread("./Figures/Figure1/dataframe_G4_consensus_motif_enrichment_species")
dataframe_G4_consensus_motif_enrichment_species_matrix <- t(dataframe_G4_consensus_motif_enrichment_species)
header <- as.character(head(dataframe_G4_consensus_motif_enrichment_species_matrix, 1))
dataframe_G4_consensus_motif_enrichment_species_df <- as.data.frame(tail(dataframe_G4_consensus_motif_enrichment_species_matrix, -1))
colnames(dataframe_G4_consensus_motif_enrichment_species_df) <- header
dataframe_G4_consensus_motif_enrichment_species_df$specie <- rownames(dataframe_G4_consensus_motif_enrichment_species_df)
dataframe_G4_consensus_motif_enrichment_species_dt <- data.table(dataframe_G4_consensus_motif_enrichment_species_df)
dataframe_G4_consensus_motif_enrichment_species_dt$median <- as.numeric(as.character(dataframe_G4_consensus_motif_enrichment_species_dt$median))
dataframe_G4_consensus_motif_enrichment_species_dt$st.dev <- as.numeric(as.character(dataframe_G4_consensus_motif_enrichment_species_dt$st.dev))
dataframe_G4_consensus_motif_enrichment_species_dt$specie <- factor(dataframe_G4_consensus_motif_enrichment_species_dt$specie , levels=dataframe_G4_consensus_motif_enrichment_species_dt[order(-median)]$specie)
Fig6.A <- ggplot(dataframe_G4_consensus_motif_enrichment_species_dt, aes(x = specie, y=median) ) +
geom_bar( stat="identity", colour="black", fill="white") +
geom_errorbar(aes(ymin = (median - st.dev), ymax = (as.numeric(median) + as.numeric(st.dev))), colour="red" , width=0.2) +
theme_bw()+
xlab("Species") +
ylab("Density (G4s / kB)") +
theme(axis.text.x = element_text(vjust = 0.7,
angle = 45))
Fig6.A
dataframe_evo_PDS_K <- fread("./Figures/Figure1/dataframe_evo_PDS_K")
dataframe_evo_PDS_K_matrix <- t(dataframe_evo_PDS_K)
header <- as.character(head(dataframe_evo_PDS_K_matrix, 1))
dataframe_evo_PDS_K_df <- as.data.frame(tail(dataframe_evo_PDS_K_matrix, -1))
colnames(dataframe_evo_PDS_K_df) <- header
dataframe_evo_PDS_K_df$Species <- rownames(dataframe_evo_PDS_K_df)
dataframe_evo_PDS_K_dt <- data.table(dataframe_evo_PDS_K_df)
dataframe_evo_PDS_K_dt_nice <- rbind(dataframe_evo_PDS_K_dt[ , .(Species=Species, Treatment="K+", median=K_median, st.dev=K_st.dev ) ],
dataframe_evo_PDS_K_dt[ , .(Species=Species, Treatment="PDS", median=PDS_median, st.dev=PDS_st.dev ) ])
dataframe_evo_PDS_K_dt_nice$median <- as.numeric(as.character(dataframe_evo_PDS_K_dt_nice$median))
dataframe_evo_PDS_K_dt_nice$st.dev <- as.numeric(as.character(dataframe_evo_PDS_K_dt_nice$st.dev))
ggplot(dataframe_evo_PDS_K_dt_nice, aes(x = Species, y=median, group=Treatment)) +
geom_bar( aes(colour=Treatment ), stat="identity", fill="white", position="dodge") +
geom_errorbar(aes(ymin = (median - st.dev), ymax = (as.numeric(median) + as.numeric(st.dev))), colour="black" , width=0.2, position = position_dodge()) +
theme_bw()+
xlab("Species") +
ylab("Density (G4s / kB)") +
theme(axis.text.x = element_text(vjust = 0.7,
angle = 45))
dataframe_evo_PDS_K_dt_nice$Species <- factor(dataframe_evo_PDS_K_dt_nice$Species , levels=dataframe_evo_PDS_K_dt_nice[Treatment=="PDS"][order(-median)]$Species)
Fig6.C <- ggplot(dataframe_evo_PDS_K_dt_nice, aes(x=Species, weight=median, ymin=median-st.dev, ymax=median+st.dev, group=Treatment)) +
geom_bar(position=position_dodge(), aes(y=median, color=Treatment), fill="white", stat="identity") +
geom_errorbar (position=position_dodge(width=0.9), colour="black", width=0.2) +
theme_bw()+
xlab("Species") +
ylab("Density (G4s / kB)") +
theme(axis.text.x = element_text(vjust = 0.7,
angle = 45))
Fig6.C
dataframe_evo_PDS_K_dt_nice
Fig1.BC <- plot_grid(Fig1.B, Fig1.C, ncol=1, labels = c("B", "C"), rel_heights = c(2, 1))
Removed 689382 rows containing non-finite values (stat_density).
Fig1 <- plot_grid(Fig1.A, Fig1.BC, nrow=1, labels = c("A", ""))
Removed 1398 rows containing missing values (geom_path).
Fig1
Fig2 <- plot_grid(Fig2.A, Fig2.B,ncol = 1 , labels ="AUTO", rel_heights = c(1.5, 1))
Removed 6792 rows containing missing values (geom_path).Removed 10788 rows containing missing values (geom_path).
Fig2
Fig3 <- plot_grid(Fig3.A, Fig3.B, Fig3.C, Fig3.D, labels = "AUTO", ncol=2)
Removed 330326 rows containing non-finite values (stat_density).Removed 610 rows containing non-finite values (stat_smooth).Removed 610 rows containing missing values (geom_point).
Fig3
Fig5.bottom <- plot_grid(Fig5.A, Fig5.B, Fig5.C, Fig5.D, nrow = 2, ncol = 2 , labels = c("B", "C", "D", "E"), rel_heights = c(1, 1, 1, 1))
Removed 2996 rows containing missing values (geom_path).Removed 2996 rows containing missing values (geom_path).
Fig5 <- plot_grid(Fig5.A1, Fig5.bottom, nrow=2, labels = c("A", ""), rel_heights = c(2, 4))
Fig5
Fig6.top <- plot_grid(Fig6.A, Fig6.C, labels = c("A", "C"))
Fig6.bottom <- plot_grid(Fig6.B, Fig6.D, labels = c("B", "D"))
Removed 9786 rows containing missing values (geom_path).Removed 4 rows containing missing values (geom_path).
Fig6 <- plot_grid(Fig6.A, Fig6.C, Fig6.B , Fig6.D, labels = c("A", "C", "B", "D") , ncol=2, rel_heights = c(1, 1, 3, 3))
Removed 9786 rows containing missing values (geom_path).Removed 4 rows containing missing values (geom_path).
Fig6 <- plot_grid(Fig6.top, Fig6.bottom, rel_heights = c(1, 1.5), nrow=2)
Fig6